Agents useful in treating facioscapulohumeral muscular dystrophy

ABSTRACT

The invention teaches antisense agents and RNA interference agents useful for treating diseases and conditions the treatment of which can benefit from reducing the expression of double homeobox 4 and/or double homeobox 4c, more particularly facioscapulohumeral muscular dystrophy. Further elaborated are methods, uses and further products employing such agents.

CROSS-REFERENCE TO RELATED APPLICATION

This application is a divisional of U.S. application Ser. No. 13/225,384filed Sep. 2, 2011 which claims the benefit of and priority to EuropeanPatent Application No. 10175125.3, entitled “Agents useful in treatingfacioscapulohumeral muscular dystrophy,” filed on Sep. 2, 2010. Bothapplications are incorporated herein by reference in their entirety.

REFERENCE TO SEQUENCE LISTING

The material in the ASCII text filed submitted on Nov. 12, 2013, isincorporated herein by reference. The ACSII text file is named “seq 1stdecle30.002d1”, created Nov. 12, 2013 and is 36 KB in size.

FIELD OF THE INVENTION

The invention generally relates to diseases and conditions the treatmentof which can benefit from reducing the expression of double homeobox 4and/or double homeobox 4c. Such diseases and conditions include interalia those comprising increased levels and/or increased activity ofdouble homeobox 4 and/or double homeobox 4c, and more particularlyinclude facioscapulohumeral muscular dystrophy. Such diseases andconditions also include those comprising expression of a fusion proteinbetween DUX4 or DUX4c and another, unrelated protein, more particularlywherein the disease or condition is a tumour, even more particularly asarcoma such as Ewing's family tumours, paediatric undifferentiated softtissue sarcomas and rhabdomyosarcomas. The invention concerns agents,more specifically antisense agents and RNA interference agents, capableof reducing or abolishing the expression of double homeobox 4 and/ordouble homeobox 4c, and elaborates methods, uses and further aspectsemploying such agents.

BACKGROUND OF THE INVENTION

Facioscapulohumeral muscular dystrophy (FSHD, FSHMD or FSH) also knownas Landouzy-Dejerine muscular dystrophy is an autosomal dominant muscledisorder affecting about 1/20,000 births. It is characterised byprogressive weakness and atrophy of the muscles from the face, theupper-arms and shoulder girdle to the lower limbs.

FSHD is genetically linked to contractions of the D4Z4 repeat array onthe 4q35 subtelomeric region. Non-affected individuals typically havebetween 11-100 copies of the 3.3-kb D4Z4 element, while FSHD patientsonly have 1-10 copies. A typical feature associated with the geneticdefect is a decrease in DNA methylation of the contracted D4Z4 array ascompared to non-affected individuals (van Overveld et al. 2005 (AnnNeurol. 58: 569-76.)). Whereas a small group of patients with a typicalFSHD phenotype does present more than 10 copies of the D4Z4 element,their DNA methylation level is low, similarly to that found incontracted D4Z4 arrays. DNA hypomethylation is typically associated withan open chromatin structure suitable for transcription (de Greef et al.2009 (Hum Mutat. 30: 1449-59)).

Gabriëls et al. 1999 (Gene 236(1): 25-32) identified the double homeobox4 (DUX4) gene within each D4Z4 element repeated in the array. The DUX4sequence was later corrected as published by Kowaljow et al. 2007(Neuromuscul Disord 17: 611-23) and is available under the NCBI Genbankaccession number: AF117653.2. Subsequent studies showed that the encodedDUX4 protein was expressed in primary myoblasts and biopsies of patientswith FSHD but not in non-affected individuals, and that the DUX4 proteinis a transcription factor targeting a large set of genes including interalia genes encoding further transcription factors, and that DUX4 geneactivation at the FSHD locus initiates a transcription cascade leadingto muscle atrophy, inflammation, decreased differentiation potential andoxidative stress, recapitulating the key features of FSHD (Bosnakowskiet al. 2008 (EMBO J 27(20): 2766-79); Kowaljow et al. 2007 (NeuromusculDisord 17: 611-23); Dixit et al. 2007 (Proc Natl Acad Sci USA 104:18157-18162)). Double homeobox 4 is thus considered a major contributorto the pathology of FSHD muscles.

Dixit et al. 2007 (supra) also demonstrated in myoblast cultures thatwhereas transcription can initiate at any D4Z4 element within the repeatarray, a prevalent stable DUX4 mRNA originates from the most distal D4Z4unit and extends into the pLAM region which flanks the telomeric side ofthe D4Z4 array, whereby the pLAM region provides the DUX4 transcriptwith an intron and a polyadenylation signal (FIGS. 1 and 2). However,also additional transcripts were identified that span several D4Z4units, may have various parts spliced out, and may also comprise thepLAM region (Snider et al. 2009. Hum Mol Genet 18: 2414-30; Coppée etal., unpublished, see FIGS. 26-28). Moreover, polymorphisms have beenfound in the pLAM region such as the presence or absence of a 1.6 kbsequence within its intron (Gabriëls et al. 1999, supra; van Deutekom etal. 2009. Hum Mutat 30: 1449-59).

Lemmers et al. 2010 (Science, August 19) propose a unifying geneticmodel for FSHD.

Furthermore, the homologous DUX4c gene was identified 42 kb centromericof the D4Z4 array, within a truncated and inverted solitary D4Z4 unit.The DUX4c gene encodes a 47-kDa protein with a double homeodomainidentical to DUX4 but divergent in the carboxyl-terminal region. TheDUX4c protein is expressed at low levels in control muscles, it isinduced in muscles of patients affected with Duchenne muscular dystrophyand is present at similar or yet higher levels in FSHD muscles.Additional experiments suggested that DUX4c could be involved inmyoblast proliferation during muscle regeneration and that changes inits expression could contribute to the FSHD pathology (Ansseau et al.2009 (PLoS One 4(10): e7482).

In certain tumour types a fusion gene is seen that includes the 3′region of the DUX4 gene as a result of chromosome rearrangements. Fusionbetween CIC, a human homolog of Drosophila capicua, and DUX4 was seen inEwing's family tumours (EFTs) (Kawamura-Saito et al. 2006. Hum Mol Genet15: 2125-2137) and paediatric undifferentiated soft tissue sarcomas(USTS) (Yoshimoto et al. 2009. Cancer Genet Cytogenet 195: 1-11), andrhabdomyosarcomas (RMS) showed fusion between the EWSR1 gene and DUX4.(Sirvent et al. 2009. Caner Genet Cytogenet 195: 12-08). As aconsequence of fusion with the C-terminal fragment of DUX4 the resultingfusion proteins acquire an enhanced transcriptional activity, whichleads to tumour formation.

SUMMARY OF THE INVENTION

The inventors postulate that down-regulating the expression of doublehomeobox 4 and/or double homeobox 4c can counteract the pathologicaleffects thereof and allows muscle regeneration to occur in FSHDpatients. The inventors further postulate that down-regulating theexpression of double homeobox 4 and/or double homeobox 4c can counteractthe enhanced transcriptional activity of DUX4-containing fusion proteinsthat is seen in certain tumours, particularly in certain types ofsarcomas, and thereby have a therapeutic benefit, e.g., slow downformation and/or progression, of such tumours.

Having conducted extensive tests the inventors realised that antisenseagents targeting sequence elements involved in splicing of DUX4 or DUX4ctranscripts can reduce or abolish the production of the respectiveproteins. This finding is unexpected, since antisense agents targetingsequence elements required for splicing were previously contemplated fortherapeutic exon skipping to at least partly restore the functionalityof defective proteins, such as for example to remove nonsense mutationsor restore the reading frame disrupted by genomic deletions orduplications in the dystrophin gene in Duchenne muscular dystrophy (DMD)(Wilton et al. 2007 (Mol Ther 15(7): 1288-96); Adams et al. 2007 (BMCMol Biol 8: 57)). Moreover, the introns of the DUX4 transcript arelocated in its 3′ untranslated region (3′ UTR), which is unusual, andinterference with splicing would therefore not be expected to alter theDUX4 coding sequence or the production of the DUX4 protein.

The inventors also realised that antisense agents targeting sequenceelements involved in polyadenylation of DUX4 or DUX4c transcripts canreduce or abolish the production of the respective proteins.

In an aspect the invention thus generally provides an antisense agentcapable of reducing or abolishing the production of DUX4 or DUX4cproteins. An antisense agent as intended herein may be capable ofbinding to (annealing with) DUX4 or DUX4c genes. In particular, suchantisense agent may be capable of binding to (annealing with) a sequenceregion in DUX4 or DUX4c (pre-mRNA) sequence.

Double homeobox 4 emerges as particularly implicated in the aetiology offacioscapulohumeral muscular dystrophy (FSHD). Hence, preferablydisclosed herein are: an antisense agent capable of reducing orabolishing the production of DUX4 protein; an antisense agent capable ofbinding to DUX4 gene; an antisense agent capable of binding to asequence region in DUX4 (pre-mRNA) sequence.

Also preferably disclosed herein are: an antisense agent capable ofreducing or abolishing the production of DUX4 protein but not of DUX4cprotein; an antisense agent capable of binding to DUX4 gene but not toDUX4c gene; an antisense agent capable of binding to a sequence regionin DUX4 (pre-mRNA) sequence but not to a sequence region in DUX4c(pre-mRNA) sequence.

In an alternative, disclosed herein are: an antisense agent capable ofreducing or abolishing the production of DUX4c protein but not of DUX4protein; an antisense agent capable of binding to DUX4c gene but not toDUX4 gene; an antisense agent capable of binding to a sequence region inDUX4c (pre-mRNA) sequence but not to a sequence region in DUX4(pre-mRNA) sequence.

In a preferred aspect the invention provides an antisense agent capableof binding to a sequence element required for splicing of the doublehomeobox 4 (DUX4) or double homeobox 4c (DUX4c) genes (as explainedelsewhere in this specification, a mention of splicing or splicing of agene generally refers to splicing of a gene's pre-mRNA to removeintervening sequence(s)). The antisense agent can reduce or abolish theproduction of the respective DUX4 or DUX4c proteins. For example andwithout being bound by any theory, such antisense agents might interferewith splicing of the DUX4 or DUX4c genes (pre-mRNA) or might act throughanother mechanism.

Double homeobox 4 emerges as particularly implicated in the aetiology offacioscapulohumeral muscular dystrophy (FSHD). Hence, preferablydisclosed herein is an antisense agent capable of binding to a sequenceelement required for splicing of the double homeobox 4 (DUX4) gene. Theantisense agent can reduce or abolish the production of DUX4 protein.

Also preferably disclosed herein is an antisense agent capable ofbinding to a sequence element required for splicing of the DUX4 gene butnot of the DUX4c gene. The antisense agent can reduce or abolish theproduction of DUX4 protein but does not reduce or abolish the productionof DUX4c protein. In an alternative, disclosed is an antisense agentcapable of binding to a sequence element required for splicing of theDUX4c gene but not of the DUX4 gene. The antisense agent can reduce orabolish the production of DUX4c protein but does not reduce or abolishthe production of DUX4 protein.

Sequence elements required for splicing of the DUX4 or DUX4c genes asintended herein particularly denote cis sequence elements, i.e., thoselocated within said DUX4 or DUX4c genes, respectively.

Sequence elements to be targeted by (i.e., selected to be bound by)antisense agents as disclosed herein may be preferably chosen from thegroup comprising or consisting of splice donor sites (i.e., 5′ splicesites), splice acceptor sites (i.e., 3′ splice sites), pyrimidine-richor polypyrimidine tracts upstream of (i.e., 5′ relative to) spliceacceptor sites, exon-intron boundaries, intron-exon boundaries, branchsites and exonic splicing enhancer elements of the DUX4 or DUX4c genes.Splice donor sites and splice acceptor sites, exon-intron boundaries andintron-exon boundaries may be readily accessible for targeting and maythus constitute preferred sequence elements as intended herein. Further,particularly effective antisense agents as disclosed herein includethose capable of binding to splice acceptor sites or intron-exonboundaries of the DUX4 or DUX4c genes.

Antisense agents as disclosed herein may preferably bind to a wholesequence element required for splicing DUX4 or DUX4c (i.e., may whollyoverlap with or wholly anneal to such sequence element). Alternatively,antisense agents as disclosed herein may bind to one or more portions ofa sequence element required for splicing DUX4 or DUX4c (e.g., may partlyoverlap with or partly anneal to such sequence element).

Reference to “binding to a sequence element required for splicing” alsoencompasses antisense agents that bind at a position sufficiently closeto said element. For example, the antisense agents may bind at aposition sufficiently close to said element to disrupt the binding andfunction of splicing machinery that would normally mediate a particularsplicing reaction occurring at that element (e.g., such agents may bindto pre-mRNA at a position within about 3, about 6, or about 9 bases ofsaid element).

In another preferred aspect the invention provides an antisense agentcapable of binding to a sequence element required for polyadenylation ofDUX4 or DUX4c genes (as explained elsewhere in this specification, amention of polyadenylation or polyadenylation of a gene generally refersto polyadenylation of a gene's pre-mRNA). The antisense agent can reduceor abolish the production of the DUX4 or DUX4c proteins. For example andwithout being bound by any theory, such antisense agents might interferewith polyadenylation of the DUX4 or DUX4c genes (pre-mRNA) or might actthrough another mechanism.

Double homeobox 4 emerges as particularly implicated in the aetiology ofFSHD. Preferably disclosed herein is thus an antisense agent capable ofbinding to a sequence element required for polyadenylation of the DUX4gene. The antisense agent can reduce or abolish the production of DUX4protein.

Also preferably disclosed herein is an antisense agent capable ofbinding to a sequence element required for polyadenylation of the DUX4gene but not of the DUX4c gene. The antisense agent can reduce orabolish the production of DUX4 protein but does not reduce or abolishthe production of DUX4c protein. In an alternative, disclosed is anantisense agent capable of binding to a sequence element required forpolyadenylation of the DUX4c gene but not of the DUX4 gene. Theantisense agent can reduce or abolish the production of DUX4c proteinbut does not reduce or abolish the production of DUX4 protein.

Also preferably disclosed herein is an antisense agent capable ofbinding to a sequence element required for polyadenylation of the DUX4gene but not capable of binding to the DUX4c gene. The antisense agentcan reduce or abolish the production of DUX4 protein but does not reduceor abolish the production of DUX4c protein. In an alternative, disclosedis an antisense agent capable of binding to a sequence element requiredfor polyadenylation of the DUX4c gene but not capable of binding to theDUX4 gene. The antisense agent can reduce or abolish the production ofDUX4c protein but does not reduce or abolish the production of DUX4protein.

Sequence elements required for polyadenylation of the DUX4 or DUX4cgenes as intended herein particularly denote cis sequence elements,i.e., those located within said DUX4 or DUX4c genes, respectively.

Sequence elements to be targeted by (i.e., selected to be bound by)antisense agents capable of binding to a sequence element required forpolyadenylation of the DUX4 or DUX4c genes may be preferablypolyadenylation signals (such as more preferably the polyadenylationsignal ATTAAA) of the DUX4 or DUX4c genes.

Antisense agents capable of binding to a sequence element required forpolyadenylation of the DUX4 or DUX4c genes may preferably bind to awhole sequence element required for polyadenylation of DUX4 or DUX4c(i.e., may wholly overlap with or wholly anneal to such sequenceelement). Alternatively, antisense agents capable of binding to asequence element required for polyadenylation of the DUX4 or DUX4c genesmay bind to one or more portions of a sequence element required forpolyadenylation of DUX4 or DUX4c (e.g., may partly overlap with orpartly anneal to such sequence element).

Reference to “binding to a sequence element required forpolyadenylation” also encompasses antisense agents that bind at aposition sufficiently close to said element (e.g., such agents may bindto pre-mRNA at a position within about 3, about 6, or about 9 bases ofsaid element).

Antisense agents as intended herein preferably comprise or denoteantisense molecules such as more preferably antisense nucleic acidmolecules or antisense nucleic acid analogue molecules. Preferably,antisense agents may refer to antisense oligonucleotides or antisenseoligonucleotide analogues. By means of an example and not limitation,such antisense agents or molecules may be between about 10 and about 100nucleotides or nucleotide analogues in length, preferably between about12 and about 80 nucleotides or nucleotide analogues in length, alsopreferably between about 15 and about 50 nucleotides or nucleotideanalogues in length, more preferably between about 20 and about 40 (suchas, e.g., between about 20 and about 30) nucleotides or nucleotideanalogues in length.

Preferably disclosed herein are antisense agents including antisensenucleic acid analogue molecules, such as, e.g., antisenseoligonucleotide analogues, more preferably antisense oligonucleotideanalogues comprising a 2′-O-methylated phosphorothioate backbone or morepreferably antisense oligonucleotide analogues comprising aphosphorodiamidate morpholino backbone as schematically illustrated inFIGS. 24 and 25, respectively. Splice-switching phosphorodiamidatemorpholino oligomers have been successfully employed to restoredystrophin expression in DMD, thereby validating this oligonucleotidechemistry (Kinali et al. 2009 (Lancet Neurol 8: 918-28)).

Advantageously, an antisense agent as disclosed herein may be conjugatedto a cell penetrating peptide (CPP) to enhance the cellular uptake ofsaid antisense agents.

Further by means of an example and not limitation, such antisense agentsor molecules may be configured to bind to (anneal with) a sequenceregion, more particularly a region in DUX4 or DUX4c (pre-mRNA) sequence,wherein said region is at least about 10 nucleotides in length,preferably at least about 12 nucleotides in length, also preferably atleast about 15 nucleotides in length, more preferably at least about 20nucleotides in length, even more preferably at least about 25 or atleast about 30 nucleotides in length, such as for example between about10 and about 100 nucleotides in length, preferably between about 12 andabout 80 nucleotides in length, also preferably between about 15 andabout 50 nucleotides in length, and more preferably between about 20 andabout 40 (such as, e.g., between about 20 and about 30) nucleotides inlength, wherein the reference to nucleotides may preferably denoteconsecutive nucleotides.

A DUX4 gene preferably intended for targeting by the antisense agents asdisclosed herein resides in the distal-most D4Z4 unit which extends intothe pLAM region flanking the telomeric side of the D4Z4 array. Such DUX4gene leads to production of comparably stable mRNA(s) (Dixit et al.2007, supra). As schematically illustrated in FIG. 2 with reference toan exemplary but non-limiting genomic sequence as shown in FIG. 3, suchDUX4 gene comprises two introns which are located in its 3′ UTR, namelyintron 1 (or intron A) within the D4Z4 unit and intron 2 (or intron B)provided by the pLAM region. Such DUX4 gene further comprises apolyadenylation signal ATTAAA located within the pLAM region.

A DUX4 gene as intended herein may also denote a DUX4 transcriptionunits that span several D4Z4 units, may display alternative splicing,and may comprise the pLAM region, in particular as disclosed by Snideret al. 2009, supra. As schematically illustrated in FIGS. 26 and 28,such DUX4 transcripts may comprise intron 1, intron ibis or intron 2awithin the D4Z4 unit, intron 2 provided by the pLAM region or intron 2abis provided by the D4Z4 unit and the pLAM region. Such DUX4 transcriptfurther comprises a polyadenylation signal ATTAAA located within thepLAM region.

Hence, sequence elements to be targeted by anti-DUX4 antisense agents asdisclosed herein, particularly sequence elements required for splicingof the DUX4 gene to be targeted by anti-DUX4 antisense agents capable ofbinding to such elements, preferably include those sequence elements(such as, e.g., splice donor sites, splice acceptor sites, exon-intronboundaries, intron-exon boundaries, pyrimidine-rich or polypyrimidinetracts, branch sites and/or exonic splicing enhancer elements) requiredfor removal of said DUX4 intron 1, intron 1 bis, intron 2, intron 2a orintron 2a bis(preferably of intron 1 or 2) upon splicing of a DUX4 gene.Preferably, the targeted DUX4 sequence elements may be chosen from thegroup comprising or consisting of splice donor sites of said DUX4 intron1, intron 1 bis, intron 2, intron 2a or intron 2a bis(preferably ofintron 1 or 2) and splice acceptor sites of said DUX4 intron 1, intron 1bis, intron 2, intron 2a or intron 2a bis (preferably of intron 1 or 2);more preferably from the group comprising or consisting of spliceacceptor sites of said DUX4 intron 1, intron 1 bis, intron 2, intron 2aor intron 2a bis(preferably of intron 1 or 2); even more preferably maybe the splice acceptor site of said DUX4 intron 2.

Sequence elements to be targeted by anti-DUX4 antisense agents asdisclosed herein, particularly sequence elements required forpolyadenylation of the DUX4 gene and to be targeted by anti-DUX4antisense agents capable of binding to such elements, preferably includethe polyadenylation signal ATTAAA.

As shown in an exemplary but non-limiting genomic sequence of the DUX4cgene (Genbank accession no. AY500824, sequence version 1, i.e.,AY500824.1), the ORF encoding the DUX4c protein is found at positions918-2042 of AY500824.1 and is not disrupted by introns. However, alarger exemplary but non-limiting genomic sequence of the DUX4c gene(Genbank accession no. NC_(—)000004, sequence version 11, i.e.,NC_(—)000004.11, range 190940254 . . . 190945505 complement) indicatesthat the DUX4c ORF may be included within a larger DUX4c transcriptcontaining six putative exons (denoted as exons 1 to 6) at respectivelypositions 1-65, 617-741, 966-1160, 1385-2945, 4034-4154 and 4911-5251 ofNC_(—)000004.11 (range 190940254 . . . 190945505, complement) (whereinputative exon 4 contains the DUX4c ORF) and corresponding five putativeintrons (denoted introns 1 to 5) at positions 66-616, 742-965,1161-1384, 2946-4033 and 4155-4910 of NC_(—)000004.11 (range 190940254 .. . 190945505, complement).

Hence, sequence elements to be targeted by anti-DUX4c antisense agentsas disclosed herein, particularly sequence elements required forsplicing of the DUX4c gene to be targeted by anti-DUX4c antisense agentscapable of binding to such elements, preferably include those sequenceelements (such as, e.g., splice donor sites, splice acceptor sites,exon-intron boundaries, intron-exon boundaries, pyrimidine-rich orpolypyrimidine tracts, branch sites and/or exonic splicing enhancerelements) required for removal of said DUX4c introns, e.g., DUX4cintrons 1, 2, 3, 4 or 5 upon splicing of such DUX4c gene. Preferably,the targeted DUX4c sequence elements may be chosen from the groupcomprising or consisting of splice donor sites of said DUX4c introns 1,2, 3, 4 or 5 and splice acceptor sites of said DUX4c introns 1, 2, 3, 4or 5; more preferably from the group comprising or consisting of spliceacceptor sites of said DUX4c introns 1, 2, 3, 4 or 5.

Without limitation, where a targeted sequence element is a splice donorsite in DUX4 or DUX4c genes, an antisense agent as disclosed herein maybe configured to bind to a region in DUX4 or DUX4c sequencecorresponding to positions about +30 to about −30, preferably about +25to about −25, more preferably about +20 to about −20 relative to therespective exon-intron boundary (i.e., position +1 denoting the lastbase of the preceding exon and position −1 denoting the first base ofthe following intron). In particular, an antisense agent may beconfigured to bind to (anneal with) at least about 10 bases, preferablyat least about 15 bases, more preferably at least about 20 bases, evenmore preferably at least about 25 bases or at least about 30 bases, suchas to between about 10 and about 40 bases or to between about 20 andabout 30 bases in any one of the above recited regions in DUX4 or DUX4csequence, wherein said reference to bases may preferably denoteconsecutive bases. Preferably, such binding (annealing) will involve atleast positions −1 or −2 (more preferably both positions −1 and −2)and/or positions +1 or +2 (more preferably both positions +1 and +2)relative to the respective exon-intron boundary. For example, suchbinding (annealing) may involve at least positions +1 to −1 or +1 to −2or +2 to −1 or +2 to −2. These positions denote bases which adjoin therespective exon-intron boundary and which are particularly relevant forsplicing. Hence, and without limitation, an antisense agent may beconfigured to bind to any one of the above recited regions in DUX4 orDUX4c sequence such that it anneals over (i.e., spans or crosses) therespective exon-intron boundary and base pairs with at least 1 base,preferably at least 2 bases, more preferably at least 5 bases and evenmore preferably at least 7 or at least 10 bases on each side of saidexon-intron boundary, such as with between 1 and about 20 bases,preferably between 2 and about 15 bases or between 2 and about 10 baseson each side of said exon-intron boundary.

Without limitation, where a targeted sequence element is a spliceacceptor site in DUX4 or DUX4c genes, an antisense agent as disclosedherein may be configured to bind to a region in DUX4 or DUX4c sequencecorresponding to positions about −30 to about +30, preferably about −25to about +25, more preferably about −20 to about +20 relative to therespective intron-exon boundary (i.e., position −1 denoting the lastbase of the preceding intron and position +1 denoting the first base ofthe following exon). In particular, an antisense agent may be configuredto bind to (anneal with) at least about 10 bases, preferably at leastabout 15 bases, more preferably at least about 20 bases, even morepreferably at least about 25 bases or at least about 30 bases, such asto between about 10 and about 40 bases or to between about 20 and about30 bases in any one of the above recited regions in DUX4 or DUX4csequence, wherein said reference to bases may preferably denoteconsecutive bases. Preferably, such binding (annealing) will involve atleast positions −1 or −2 (more preferably both positions −1 and −2)and/or positions +1 or +2 (more preferably both positions +1 and +2)relative to the respective intron-exon boundary. For example, suchbinding (annealing) may involve at least positions −1 to +1 or −1 to +2or −2 to +1 or −2 to +2. These positions denote bases which adjoin therespective intron-exon boundary and which are particularly relevant forsplicing. Hence, and without limitation, an antisense agent may beconfigured to bind to any one of the above recited regions in DUX4 orDUX4c sequence such that it anneals over (i.e., spans or crosses) therespective intron-exon boundary and base pairs with at least 1 base,preferably at least 2 bases, more preferably at least 5 bases and evenmore preferably at least 7 or at least 10 bases on each side of saidintron-exon boundary, such as with between 1 and about 20 bases,preferably between 2 and about 15 bases or between 2 and about 10 baseson each side of said intron-exon boundary.

In an example, an anti-DUX4 antisense agent may be configured to bind to(anneal with) at least about 10 bases, preferably at least about 15bases, more preferably at least about 20 bases, even more preferably atleast about 25 bases or at least about 30 bases, such as to betweenabout 10 and about 40 bases or to between about 20 and about 30 bases,preferably wherein said reference to bases denotes consecutive bases, ofany one of the following DUX4 sequences (SEQ ID NO: 2 to 9) or ofvariants thereof having at least about 80% and preferably at least about90% or at least about 95% sequence identity to the respective sequences:

ggctctgctggaggagctttaggacgcggg|gttgggacggggtcgggtggttcggggcag (SEQ IDNO: 2; positions +30 to −30 of an exemplary DUX4 exon 1-intron 1boundary; the intron sequence is in italics);

gaggagctttaggacgcggg|gttgggacggggtcgggtgg (SEQ ID NO: 3; positions +20to −20 of an exemplary DUX4 exon 1-intron 1 boundary; the intronsequence is in italics);

gctgaccggcctgggattcctgccttctag|gctaggcccggtgagagactccacaccgc (SEQ ID NO:4; positions −30 to +30 of an exemplary DUX4 intron 1-exon 2 boundary;the intron sequence is in italics);

ctgggattcctgccttctag|gctaggcccggtgagagac (SEQ ID NO: 5; positions −20 to+20 of an exemplary DUX4 intron 1-exon 2 boundary; the intron sequenceis in italics);

ggcatcccggggatcccagagccggcccag|gtacctgcgcacgcgcgggtttgcgggcag (SEQ IDNO: 6; positions +30 to −30 of an exemplary DUX4 exon 2-intron 2boundary; the intron sequence is in italics);

ggatcccagagccggcccag|gtacctgcgcacgcgcgggt (SEQ ID NO: 7; positions +20to −20 of an exemplary DUX4 exon 2-intron 2 boundary; the intronsequence is in italics);

tctgtctgtctttgcccgcttcctggctag|acctgcgcgcagtgcgcaccccggctgacg (SEQ IDNO: 8; positions −30 to +30 of an exemplary DUX4 intron 2-exon 3boundary; the intron sequence is in italics).

tttgcccgcttcctggctag|acctgcgcgcagtgcgcacc (SEQ ID NO: 9; positions −20to +20 of an exemplary DUX4 intron 2-exon 3 boundary; the intronsequence is in italics).

Preferably, the anti-DUX4 antisense agent is capable of annealing over(i.e., span or cross) the respective exon-intron or intron-exonboundaries found in SEQ ID NO: 2 to 9 or in the variants thereof(indicated by the “|” symbol above). Also preferably, the anti-DUX4antisense agent is capable of annealing with at least one and preferablyboth of the two intronic bases (indicated above in bold italics)adjacent to the respective exon-intron or intron-exon boundaries and/or(preferably “and”) with at least one and preferably both of the twoexonic bases (underlined above) adjacent to the respective exon-intronor intron-exon boundaries.

In non-limiting embodiments, an effective anti-DUX4 antisense agent maybe configured to bind to (anneal with) any one of the following DUX4sequences (SEQ ID NO: 10 to 15, 66) or to variants thereof having atleast about 80% and preferably at least about 90% or at least about 95%sequence identity to the respective sequences, or to fragments thereofcomprising at least 10 bases, or at least 12 bases, preferably at leastabout 15 bases, more preferably at least about 20 bases, even morepreferably at least about 25 bases, preferably wherein said reference tobases denotes consecutive bases, of the respective sequences orvariants. More specifically, such an anti-DUX4 antisense agent maycomprise, consist essentially of or consist of a sequence (e.g., anucleic acid sequence or nucleic acid analogue sequence) complementaryto any one of said DUX4 sequences SEQ ID NO: 10 to 15, 66 or to variantsthereof having at least about 80% and preferably at least about 90% orat least about 95% sequence identity to the respective sequences, or tofragments thereof comprising at least 10 bases, or at least 12 bases,preferably at least about 15 bases, more preferably at least about 20bases, even more preferably at least about 25 bases, preferably whereinsaid reference to bases denotes consecutive bases, of the respectivesequences or variants:

cttctaggtctaggcccggtgagag (SEQ ID NO: 10; positions −7 to +18 of anexemplary DUX4 intron 1-exon 2 boundary; positions 12241-12265 ofGenbank sequence AF117653.2 (see FIG. 3); the intron sequence is initalics);

tggctagacctgcgcgcagtgcgca (SEQ ID NO: 11; positions −7 to +18 of anexemplary DUX4 intron 2-exon 3 boundary; positions 12678-12702 ofAF117653.2; the intron sequence is in italics);

cttcctggctagacctgcgcgcagt (SEQ ID NO: 12; positions −12 to +13 of anexemplary DUX4 intron 2-exon 3 boundary; positions 12673-12697 ofAF117653.2; the intron sequence is in italics);

agacctgcgcgcagtgcgcaccccg (SEQ ID NO: 13; positions −2 to +23 of anexemplary DUX4 intron 2-exon 3 boundary; positions 12685-12703 ofAF117653.2; the intron sequence is in italics);

cttcctggctagacctgcgcgcagtgcgca (SEQ ID NO: 14; positions −12 to +18 ofan exemplary DUX4 intron 2-exon 3 boundary; positions 12673-12702 ofAF117653.2; the intron sequence is in italics);

gcccgcttcctggctagacctgcgcgcagt (SEQ ID NO: 15; positions −17 to +13 ofan exemplary DUX4 intron 2-exon 3 boundary; positions 12668-12697 ofAF117653.2; the intron sequence is in italics).

acgcggggttgggacggggtcgggt (SEQ ID NO: 66; positions +7 to −18 of anexemplary DUX4 exon 1-intron 1 boundary; positions 12105-12129 ofAF117653.2; the intron sequence is in italics).

For example, disclosed herein are anti-DUX4 antisense agents comprising,consisting essentially of or consisting of any one of sequences (e.g.,nucleic acid sequences or nucleic acid analogue sequences) SEQ ID NO: 16to 21, 64 or variants thereof having at least about 80% and preferablyat least about 90% or at least about 95% sequence identity to therespective sequences, or fragments thereof comprising at least 10 bases,or at least 12 bases, preferably at least about 15 bases, morepreferably at least about 20 bases, even more preferably at least about25 bases, preferably wherein said reference to bases denotes consecutivebases, of the respective sequences or variants:

(SEQ ID NO: 16) CUCUCACCGGGCCUAGACCUAGAAG; (SEQ ID NO: 17)UGCGCACUGCGCGCAGGUCUAGCCA; (SEQ ID NO: 18) ACUGCGCGCAGGUCUAGCCAGGAAG;(SEQ ID NO: 19) CGGGGUGCGCACUGCGCGCAGGUCU; (SEQ ID NO: 20)UGCGCACUGCGCGCAGGUCUAGCCAGGAAG; (SEQ ID NO: 21)ACUGCGCGCAGGUCUAGCCAGGAAGCGGGC; (SEQ ID NO: 64)ACCCGACCCCGUCCCAACCCCGCGU;

wherein U denotes uracil (which may be optionally replaced by thymine,T). In particular, the anti-DUX4 antisense agents comprising, consistingessentially of or consisting of any one of sequences SEQ ID NO: 16 to21, 64 or the variants or fragments thereof display complementarity to,and are hence configured to bind to (anneal with), the above DUX4sequences SEQ ID NO: 10 to 15, 66 or the variants or fragments thereof.

In an example, an anti-DUX4c antisense agent may be configured to bindto (anneal with) at least about 10 bases, preferably at least about 15bases, more preferably at least about 20 bases, even more preferably atleast about 25 bases or at least about 30 bases, such as to betweenabout 10 and about 40 bases or to between about 20 and about 30 bases,preferably wherein said reference to bases denotes consecutive bases, ofany one of the following DUX4c sequences (SEQ ID NO: 22 to 41) or ofvariants thereof having at least about 80% and preferably at least about90% or at least about 95% sequence identity to the respective sequences:

acctccccacagcccacagacttgtcata|gtgcgggaatagtgttctatcactacagga (SEQ ID NO:22; positions +30 to −30 of an exemplary putative DUX4c exon 1-intron 1boundary; positions 36-95 of Genbank sequence NC_(—)000004.11 range190940254.190945505, complement; the intron sequence is in italics);

agcccacagctcttgtcata|gtgcgggaatagtgttctat (SEQ ID NO: 23; positions +20to −20 of said exemplary DUX4c exon 1-intron 1 boundary; the intronsequence is in italics);

gcagagaggaaagcggtcttccgcctccag|ggccagcgggacctcgcactccgggaaaac (SEQ IDNO: 24; positions −30 to +30 of an exemplary putative DUX4c intron1-exon 2 boundary; positions 587-646 of NC_(—)000004.11 range190940254.190945505, complement; the intron sequence is in italics);

aagcggtcaccgcctccag|ggccagcgggacctcgcact (SEQ ID NO: 25; positions −20to +20 of said exemplary DUX4c intron 1-exon 2 boundary; the intronsequence is in italics);

gctcaccagccctccggatcgccggcccgg|gtcacttcatcccggagcaattcggacgaa (SEQ IDNO: 26; positions +30 to −30 of an exemplary putative DUX4c exon2-intron 2 boundary; positions 712-771 of NC_(—)000004.11 range190940254.190945505, complement; the intron sequence is in italics);

cctccggatcgccggcccgg|gtcacttcatcccggagcaa (SEQ ID NO: 27; positions +20to −20 of said exemplary DUX4c exon 2-intron 2 boundary; the intronsequence is in italics);

cgggaccacgctccacgccctctgcaag|gggacctgdgctcgcgtgtctcccgcccc (SEQ ID NO:28; positions −30 to +30 of an exemplary putative DUX4c intron 2-exon 3boundary; positions 936-995 of NC_(—)000004.11 range190940254.190945505, complement; the intron sequence is in italics);

gctccacgccctctgcaag|gggacctgttgctcgcgtgt (SEQ ID NO: 29; positions −20to +20 of said exemplary DUX4c intron 2-exon 3 boundary; the intronsequence is in italics);

ttgcaggaaacaggaatccgtggtcaggcc|gtgatgcacccgacgtttcttttctctgca (SEQ IDNO: 30; positions +30 to −30 of an exemplary putative DUX4c exon3-intron 3 boundary; positions 1131-1190 of NC_(—)000004.11 range190940254.190945505, complement; the intron sequence is in italics);

caggaatccgtggtcaggcc|gtgatgcacccgacgtttct (SEQ ID NO: 31; positions +20to −20 of said exemplary DUX4c exon 3-intron 3 boundary; the intronsequence is in italics);

agtcaagacagcggcttccagtttccatag|aattactggagaacctcagagagccagccc (SEQ IDNO: 32; positions −30 to +30 of an exemplary putative DUX4c intron3-exon 4 boundary; positions 1355-1414 of NC_(—)000004.11 range190940254.190945505, complement; the intron sequence is in italics);

gcggcaccagtaccatag|aattactggagaacctcaga (SEQ ID NO: 33; positions −20 to+20 of said exemplary DUX4c intron 3-exon 4 boundary; the intronsequence is in italics);

gaagaacaccgggctctgctggaggagcag|gttggagcggggttggggcggggtgggggc (SEQ IDNO: 34; positions +30 to −30 of an exemplary putative DUX4c exon4-intron 4 boundary; positions 2916-2975 of NC_(—)000004.11 range190940254.190945505, complement; the intron sequence is in italics);

gggctctgctggaggagcag|gttggagcggggttggggcg (SEQ ID NO: 35; positions +20to −20 of said exemplary DUX4c exon 4-intron 4 boundary; the intronsequence is in italics);

ctggattccacgtactagccctctgcag|aggtgcctgdgctcaagtctctgcccccg (SEQ ID NO:36; positions −30 to +30 of an exemplary putative DUX4c intron 4-exon 5boundary; positions 3404-4063 of NC_(—)000004.11 range190940254.190945505, complement; the intron sequence is in italics);

cgtactagccctctgcag|aggtgcctgdgctcaagtc (SEQ ID NO: 37; positions −20 to+20 of said exemplary DUX4c intron 4-exon 5 boundary; the intronsequence is in italics);

ttccaggaatgcgtggaacaccagcatcgt|gtcggtgctctcctttccagtttcaaacag (SEQ IDNO: 38; positions +30 to −30 of an exemplary putative DUX4c exon5-intron 5 boundary; positions 4125-4184 of NC_(—)000004.11 range190940254.190945505, complement; the intron sequence is in italics);

gcgtggaacaccagcatcgt|gtcggtgctctcctttccag (SEQ ID NO: 39; positions +20to −20 of said exemplary DUX4c exon 5-intron 5 boundary; the intronsequence is in italics);

ctgtcctcttggtgctgtgggtcctgaaag|ttgtcgagtgcgcccgtccctgtggtggga (SEQ IDNO: 40; positions −30 to +30 of an exemplary putative DUX4c intron5-exon 6 boundary; positions 4881-4940 of NC_(—)000004.11 range190940254.190945505, complement; the intron sequence is in italics);

ggtgctgtgggtcctgaaag|ttgtcgagtgcgcccgtccc (SEQ ID NO: 41; positions −20to +20 of said exemplary DUX4c intron 5-exon 6 boundary; the intronsequence is in italics).

Preferably, the anti-DUX4c antisense agent is capable of annealing over(i.e., span or cross) the respective exon-intron or intron-exonboundaries found in SEQ ID NO: 22 to 41 or in the variants thereof(indicated by the “|” symbol above). Also preferably, the anti-DUX4cantisense agent is capable of annealing with at least one and preferablyboth of the two intronic bases (indicated above in bold italics)adjacent to the respective exon-intron or intron-exon boundaries and/or(preferably “and”) with at least one and preferably both of the twoexonic bases (underlined above) adjacent to the respective exon-intronor intron-exon boundaries.

Without limitation, where a targeted sequence element is apolyadenylation signal in the DUX4 or DUX4c gene, such as preferably thepolyadenylation signal ATTAAA, an antisense agent as disclosed hereinmay be configured to bind to a region in DUX4 or DUX4c sequencecorresponding to positions about −30 to about +30, preferably about −25to about +25, more preferably about −20 to about +20 relative to saidpolyadenylation signal (i.e., position −1 denoting the last basepreceding the polyadenylation signal and position +1 denoting the firstbase following the polyadenylation signal). In particular, suchantisense agent may be configured to bind to (anneal with) at leastabout 10 bases, preferably at least about 15 bases, more preferably atleast about 20 bases, even more preferably at least about 25 bases or atleast about 30 bases, such as to between about 10 and about 40 bases orto between about 20 and about 30 bases in any one of the above recitedregions in the DUX4 or DUX4c sequence, wherein said reference to basesmay preferably denote consecutive bases. Preferably, the antisense agentmay be configured to bind such that it anneals with at least a portionof (e.g., 1, 2, 3, 4, 5 or 6 nucleotides) the polyadenylation signal orwith the entire polyadenylation signal. For example but withoutlimitation, such antisense agent may be configured to anneal over (i.e.,to span or cross) the polyadenylation signal and to base pair with atleast 1 base, preferably at least 2 bases, more preferably at least 5bases and even more preferably at least 7 or at least 10 bases on eachside of said polyadenylation signal, such as with between 1 and about 20bases, preferably between 2 and about 15 bases or between 2 and about 10bases on each side of said polyadenylation signal.

In an example, an anti-DUX4 antisense agent may be configured to bind to(anneal with) at least about 10 bases, preferably at least about 15bases, more preferably at least about 20 bases, even more preferably atleast about 25 bases or at least about 30 bases, such as to betweenabout 10 and about 40 bases or to between about 20 and about 30 bases,preferably wherein said reference to bases denotes consecutive bases, ofthe following DUX4 sequences (SEQ ID NO: 67 or 68) or of variantsthereof having at least about 80% and preferably at least about 90% orat least about 95% sequence identity to the respective sequences:

acatctcctggatgattagttcagagatatattaaaatgccccctccctgtggatcctatagaaga (SEQID NO: 67; positions −30 to +30 of an exemplary DUX4 polyadenylationsignal; the polyadenylation signal is in italics);

gatgattagttcagagatatattaaaatgccccctccctgtggatc (SEQ ID NO: 68; positions−20 to +20 of an exemplary DUX4 polyadenylation signal; thepolyadenylation signal is in italics);

Preferably, the anti-DUX4 antisense agent may be capable of annealingover (i.e., span or cross) the polyadenylation signal ATTAAA found inSEQ ID NO: 67 or 68 or in the variants thereof.

In non-limiting embodiments, an effective anti-DUX4 antisense agent maybe configured to bind to (anneal with) the following DUX4 sequence (SEQID NO: 69) or to variants thereof having at least about 80% andpreferably at least about 90% or at least about 95% sequence identity tosaid sequence, or to fragments thereof comprising at least 10 bases, orat least 12 bases, preferably at least about 15 bases, more preferablyat least about 20 bases, even more preferably at least about 25 bases,preferably wherein said reference to bases denotes consecutive bases, ofsaid sequence or variants. More specifically, such an anti-DUX4antisense agent may comprise, consist essentially of or consist of asequence (e.g., a nucleic acid sequence or nucleic acid analoguesequence) complementary to said DUX4 sequences SEQ ID NO: 69 or tovariants thereof having at least about 80% and preferably at least about90% or at least about 95% sequence identity to said sequence, or tofragments thereof comprising at least 10 bases, or at least 12 bases,preferably at least about 15 bases, more preferably at least about 20bases, even more preferably at least about 25 bases, preferably whereinsaid reference to bases denotes consecutive bases, of the respectivesequences or variants:

agttcagagatatattaaaatgccc (SEQ ID NO: 69; positions −13 to +6 of anexemplary DUX4 polyadenylation signal; positions 12839-12863 of Genbanksequence AF117653.2 (see FIG. 3); the polyadenylation signal is initalics);

For example, disclosed herein is an anti-DUX4 antisense agentscomprising, consisting essentially of or consisting of sequence (e.g.,nucleic acid sequences or nucleic acid analogue sequences) SEQ ID NO: 65or variants thereof having at least about 80% and preferably at leastabout 90% or at least about 95% sequence identity to said sequence, orfragments thereof comprising at least 10 bases, or at least 12 bases,preferably at least about 15 bases, more preferably at least about 20bases, even more preferably at least about 25 bases, preferably whereinsaid reference to bases denotes consecutive bases, of said sequence orvariants:

(SEQ ID NO: 65) GGGCAUUUUAAUAUAUCUCUGAACU

wherein U denotes uracil (which may be optionally replaced by thymine,T). In particular, the anti-DUX4 antisense agents comprising, consistingessentially of or consisting of any one of sequence SEQ ID NO: 65 or thevariants or fragments thereof display complementarity to, and are henceconfigured to bind to (anneal with), the above DUX4 sequences SEQ ID NO:69 or the variants or fragments thereof.

In a further aspect the invention provides an RNA interference (RNAi)agent capable of reducing or abolishing the production of DUX4 and/orDUX4c proteins.

In particular, the RNAi agent may be configured to target DUX4 and/orDUX4c messenger RNA (mRNA), respectively. Whereas the RNAi agent may beconfigured to target any part of DUX4 and/or DUX4c mRNA, such as forexample the 5′-untranslated region (5′ UTR), ORF or 3′ UTR thereof, theRNAi agent may be preferably configured to target the 3′ UTR of DUX4and/or DUX4c mRNA. The inventors realised that targeting the 3′UTR ofDUX4 and/or DUX4c mRNA allows for particularly effective RNAi-mediateddownregulation of the production of DUX4 and/or DUX4c proteins.Moreover, targeting the 3′UTR of DUX4 or DUX4c mRNA allows for RNAiagents which are highly specific for either DUX4 or DUX4c mRNA,presumably but without limitation due to sequence differences in thedistinct 3′UTRs.

DUX4 emerges as particularly implicated in the aetiology of FSHD. Hence,preferably disclosed herein is an RNAi agent capable of reducing orabolishing the production of DUX4 protein. Such RNAi agent is configuredto target DUX4 mRNA.

Also preferably disclosed herein is an RNAi agent capable of reducing orabolishing the production of DUX4 protein but not of the DUX4c protein.Such RNAi agent is configured to target DUX4 mRNA but not DUX4c mRNA. Inan alternative, disclosed is an RNAi agent capable of reducing orabolishing the production of DUX4c protein but not of the DUX4 protein.Such RNAi agent is configured to target DUX4c mRNA but not DUX4 mRNA.

RNAi agents as intended herein may particularly comprise or denote(i.e., may be selected from a group comprising or consisting of) RNAinucleic acid molecules or RNAi nucleic acid analogue molecules, such aspreferably short interfering nucleic acids and short interfering nucleicacid analogues (siNA) such as short interfering RNA and shortinterfering RNA analogues (siRNA), and may further denote inter aliadouble-stranded RNA and double-stranded RNA analogues (dsRNA), micro-RNAand micro-RNA analogues (miRNA), and short hairpin RNA and short hairpinRNA analogues (shRNA).

Advantageously, an RNAi agent as disclosed herein may be conjugated to acell penetrating peptide (CPP), to enhance the cellular uptake of saidRNAi agents.

An RNAi agent typically includes a double stranded portion(notwithstanding the optional and potentially preferred presence of anysingle-stranded overhands) comprising at least 16 bases, preferably atleast 17 bases, more preferably at least 18 bases and still morepreferably at least 19 bases, and usually between 18 and 35 bases,preferably between 19 and 30 bases, more preferably between 20 and 25bases and even more preferably between 21 and 23 bases which areidentical or almost identical to (e.g., showing 90% or more, e.g., atleast 95%, sequence identity to, or showing maximum 2 and preferablyonly 1 mismatch with) an mRNA whose silencing is desired and which isthus targeted by said RNAi agent (such as, e.g., DUX4 and/or DUX4cmRNAs).

A DUX4 gene preferably intended for targeting by the RNAi agents asdisclosed herein resides in the distal-most D4Z4 unit which extends intothe pLAM region flanking the telomeric side of the D4Z4 array. Such DUX4gene leads to production of comparably stable mRNA(s) (Dixit et al.2007, supra). As schematically illustrated in FIG. 2 with reference toan exemplary but non-limiting genomic sequence as shown in FIG. 3, suchDUX4 gene comprises two introns which are located in its 3′ UTR, namelyintron 1 (or intron A) within the D4Z4 unit and intron 2 (or intron B)provided by the pLAM region. Alternative splicing of intron 1 asschematically captured in FIG. 2 leads to alternative DUX4 mRNAs.

Exemplary but non-limiting DUX4 cDNA sequences including or not intron 1are shown in FIGS. 4 (SEQ ID NO: 42) and 5 (SEQ ID NO: 43),respectively.

Accordingly, in an embodiment anti-DUX4 RNAi agents as intended hereinmay be configured to target DUX4 mRNA as represented by the DUX4 cDNAsequence set forth in SEQ ID NO: 42 or variants thereof having at leastabout 80% and preferably at least about 90% or at least about 95%sequence identity to SEQ ID NO: 42. Preferably, such anti-DUX4 RNAiagents may be configured to target the 3′ UTR of said DUX4 mRNA orvariants, such as for example to target 3′ UTR sequences correspondingto or overlapping with exon 1, intron 1, exon 2 and/or exon 3.

In another embodiment anti-DUX4 RNAi agents as intended herein may beconfigured to target DUX4 mRNA as represented by the DUX4 cDNA sequenceset forth in SEQ ID NO: 43 or variants thereof having at least about 80%and preferably at least about 90% or at least about 95% sequenceidentity to SEQ ID NO: 43. Preferably, such anti-DUX4 RNAi agents may beconfigured to target the 3′ UTR of said DUX4 mRNA or variants, such asfor example to target 3′ UTR sequences corresponding to or overlappingwith exon 1, exon 2 and/or exon 3.

In an example, an anti-DUX4 RNAi agent may be configured to target anyone of the following DUX4 mRNA sequences (SEQ ID NO: 44 to 46) orvariants thereof having at least about 80% and preferably at least about90% or at least about 95% sequence identity to the respective sequences,or fragments thereof comprising at least 16 bases, preferably at least17 bases, more preferably at least 18 bases and still more preferably atleast 19 bases, and usually between 18 and 35 bases, preferably between19 and 30 bases, more preferably between 20 and 25 bases and even morepreferably between 21 and 23 bases, preferably wherein said reference tobases denotes consecutive bases, of the respective sequences orvariants:

(SEQ ID NO: 44) CGCGGGGAACACCUGGCUGGCUACGGAGGGGCGUG (SEQ ID NO: 45)GCCUUCUAGGUCUAGGCCCGGUGAGAGACUCCACA (SEQ ID NO: 46)UAGGCAAACCUGGAUUAGAGUUACAUCUCCUGGAU

wherein U denotes uracil (which may be optionally replaced by thymine,T).

In exemplary but non-limiting embodiments, an anti-DUX4 RNAi agent asdisclosed herein may comprise any one of the following sequences (SEQ IDNO: 47 to 49) or variants thereof having at least about 80% andpreferably at least about 90% or at least about 95% sequence identity to(e.g., variants showing maximum 2 and preferably only 1 mismatch with)the respective sequences, or fragments thereof comprising at least 16bases, preferably at least 17 bases and more preferably at least 18bases, preferably wherein said reference to bases denotes consecutivebases, of the respective sequences or variants:

(SEQ ID NO: 47) acaccuggcuggcuacgga; (SEQ ID NO: 48)ggucuaggcccggugagag; (SEQ ID NO: 49) ccuggauuagaguuacauc.

wherein U denotes uracil (which may be optionally replaced by thymine,T).

Exemplary but non-limiting DUX4c cDNA sequences are shown in FIGS. 6(SEQ ID NO: 50) and 7 (SEQ ID NO: 51), including 3′ UTR regions ofdistinct lengths.

Accordingly, in an embodiment anti-DUX4c RNAi agents as intended hereinmay be configured to target DUX4c mRNA as represented by the DUX4c cDNAsequence set forth in SEQ ID NO: 50 or variants thereof having at leastabout 80% and preferably at least about 90% or at least about 95%sequence identity to SEQ ID NO: 50. Preferably, such anti-DUX4c RNAiagents may be configured to target the 3′ UTR of said DUX4c mRNA orvariants.

In another embodiment anti-DUX4c RNAi agents as intended herein may beconfigured to target DUX4c mRNA as represented by the DUX4c cDNAsequence set forth in SEQ ID NO: 51 or variants thereof having at leastabout 80% and preferably at least about 90% or at least about 95%sequence identity to SEQ ID NO: 51. Preferably, such anti-DUX4c RNAiagents may be configured to target the 3′ UTR of said DUX4c mRNA orvariants.

As noted above, a further exemplary but non-limiting genomic sequence ofthe DUX4c gene (Genbank accession no. NC_(—)000004 range190940254.190945505, complement, sequence version 11, i.e.,NC_(—)000004.11 range 190940254.190945505, complement) predicts a longerDUX4c mRNA than those shown in FIGS. 6 and 7. In particular, suchfurther exemplary but non-limiting DUX4c cDNA sequence is available inthe Genbank database under accession no. XR_(—)041199 (sequences version2, i.e., XR_(—)041199.2) and reproduced in FIG. 8 (SEQ ID NO: 52).

Hence, in an embodiment anti-DUX4c RNAi agents as intended herein may beconfigured to target DUX4c mRNA as represented by the DUX4c cDNAsequence set forth in SEQ ID NO: 52 or variants thereof having at leastabout 80% and preferably at least about 90% or at least about 95%sequence identity to SEQ ID NO: 52. Preferably, such anti-DUX4c RNAiagents may be configured to target the 3′ UTR of said DUX4c mRNA orvariants.

In an example, an anti-DUX4c RNAi agent may be configured to target anyone of the following DUX4c mRNA sequences (SEQ ID NO: 53 to 55) orvariants thereof having at least about 80% and preferably at least about90% or at least about 95% sequence identity to the respective sequences,or fragments thereof comprising at least 16 bases, preferably at least17 bases, more preferably at least 18 bases and still more preferably atleast 19 bases, and usually between 18 and 35 bases, preferably between19 and 30 bases, more preferably between 20 and 25 bases and even morepreferably between 21 and 23 bases, preferably wherein said reference tobases denotes consecutive bases, of the respective sequences orvariants:

(SEQ ID NO: 53) uguagacaccagaguuucagcaaaaggcacgaccu (SEQ ID NO: 54)cacacagaggagggcugucauucuuuccugagcau (SEQ ID NO: 55)uuuccccagcguucuucagucgaguuggcggagac

wherein U denotes uracil (which may be optionally replaced by thymine,T).

In exemplary but non-limiting embodiments, an anti-DUX4c RNAi agent asdisclosed herein may comprise any one of the following sequences (SEQ IDNO: 56 to 58) or variants thereof having at least about 80% andpreferably at least about 90% or at least about 95% sequence identity to(e.g., variants showing maximum 2 and preferably only 1 mismatch with)the respective sequences, or fragments thereof comprising at least 16bases, preferably at least 17 bases and more preferably at least 18bases, preferably wherein said reference to bases denotes consecutivebases, of the respective sequences or variants:

(SEQ ID NO: 56) ccagaguuucagcaaaagg; (SEQ ID NO: 57)ggagggcugucauucuuuc; (SEQ ID NO: 58) gcguucuucagucgaguug;

wherein U denotes uracil (which may be optionally replaced by thymine,T).

Also disclosed herein is a method for producing any one anti-DUX4 and/oranti-DUX4c antisense agent or RNAi agent as taught herein, particularlywherein said agent comprises, consists essentially of or consists of anucleic acid molecule or a nucleic acid analogue molecule, comprisingsynthesising said agent from its constituent nucleotides or nucleotideanalogues, and optionally and preferably at least partly purifying theagent from the synthesis reaction.

Further disclosed herein is a nucleic acid, more specifically anisolated nucleic acid, encoding any one or more anti-DUX4 and/oranti-DUX4c antisense agent or RNAi agent as taught herein. Preferably,the nucleic acid may be operably linked to one or more regulatorysequences allowing for expression of the nucleic acid in an expressionsystem, such as without limitation in vitro (e.g., in a cell-freeexpression system) or in a host cell or host organism.

As well disclosed is a recombinant nucleic acid construct (i.e., avector) comprising a nucleic acid encoding any one or more anti-DUX4and/or anti-DUX4c antisense agent or RNAi agent as taught herein. Suchconstruct (vector) may allow inter alia to propagate the nucleic acidencoding said agent, e.g., in vitro or in a host cell or host organism.Also contemplated is a method for producing said recombinant nucleicacid construct (vector) comprising introducing the nucleic acid encodingsaid agent to a recipient nucleic acid construct (recipient vector).

Preferably, the recombinant nucleic acid construct may be an expressionconstruct (i.e., an expression vector), hence may be capable ofexpressing (configured to express) the nucleic acid encoding the one ormore anti-DUX4 and/or anti-DUX4c antisense agent or RNAi agent in anexpression system, such as without limitation in vitro (e.g., in acell-free expression system) or in a host cell or host organism. In anexpression construct (expression vector), the nucleic acid encoding saidagent is operably linked to one or more regulatory sequences allowingfor expression of the nucleic acid in said expression system. Alsocontemplated is thus a method for producing said expression construct(expression vector) comprising introducing the nucleic acid encodingsaid agent to a recipient expression construct (recipient expressionvector).

Also disclosed is thus a method for producing any one or more anti-DUX4and/or anti-DUX4c antisense agent or RNAi agent as taught hereincomprising expressing said agent from an expression construct(expression vector) as taught herein comprising a nucleic acid encodingsaid agent, in an expression system, and optionally at least partlypurifying the agent.

Disclosed herein is as well a host cell comprising any one or moreanti-DUX4 and/or anti-DUX4c antisense agent or RNAi agent, or anisolated nucleic acid encoding such an agent, or a recombinant construct(vector) (preferably an expression construct, expression vector)comprising a nucleic acid encoding such an agent, as taught herein. Alsoencompassed is a method for producing such a host cell comprisingintroducing into a recipient host cell the anti-DUX4 and/or anti-DUX4cantisense agent or RNAi agent, or the isolated nucleic acid encodingsuch an agent, or the recombinant construct (vector) (preferably anexpression construct, expression vector) comprising a nucleic acidencoding such an agent. Preferably, the host cell may be a prokaryoticor eukaryotic cell, more preferably a bacterial, fungal, plant or animalcell, even more preferably a mammal cell or a primate cell, includingvery preferably human cells, as well as non-human mammal cells andnon-human primate cells. For example, said human host cell may be amyoblast or a myoblast precursor derived from a patient, such as forexample a myoblast derived from a muscle biopsy of said patient orderived from a mesangioblast of said patient, or said myoblast ormyoblast precursor may be differentiated from an adult stem cell or aninduced pluripotent stem (iPS) cell of said patient. The isolatednucleic acid or construct (vector) may be integrated, preferably stablyintegrated, into the genome of the host cell or may remain extra-genomicor extra-chromosomal. Insofar the host cell comprises said agent,isolated nucleic acid or construct (vector), it may be denoted a‘transgenic’ or ‘transformed’ cell in that regard. Preferably, a hostcell expresses or is under suitable conditions capable of expressing theisolated nucleic acid or vector comprised therein, thereby producing theanti-DUX4 and/or anti-DUX4c antisense agent or RNAi agent encodedthereby. Also contemplated is thus a method for producing any one ormore anti-DUX4 and/or anti-DUX4c antisense agent or RNAi agent as taughtherein comprising culturing or maintaining a host cell comprising anisolated nucleic acid encoding said agent or an expression construct(expression vector) comprising a nucleic acid encoding said agent, underconditions conducive to expression of said agent from said isolatednucleic acid or expression construct. The so-produced agent may beintended to exert its silencing effect in the host cell expressing it,or may by intended for use elsewhere in which case the method mayfurther optionally and preferably comprise at least partly purifying theagent.

Disclosed herein is as well a host organism comprising any one or moreanti-DUX4 and/or anti-DUX4c antisense agent or RNAi agent, or anisolated nucleic acid encoding such an agent, or a recombinant construct(vector) (preferably an expression construct, expression vector)comprising a nucleic acid encoding such an agent, or a host cell, astaught herein. Also encompassed is a method for producing such a hostorganism comprising introducing the anti-DUX4 and/or anti-DUX4cantisense agent or RNAi agent, or the isolated nucleic acid encodingsuch an agent, or the recombinant construct (vector) (preferably anexpression construct, expression vector) comprising a nucleic acidencoding such an agent, into a recipient host organism, e.g., to a cell,tissue or organ of said host organism, or introducing the host cell astaught herein to a recipient host organism, or at least partlyregenerating an organism from said host cell. Preferably, the hostorganism may be a multi-cellular organism, more preferably a plant oranimal organism, even more preferably a mammal or primate, particularlyincluding non-human mammals and non-human primates. The isolated nucleicacid or construct (vector) may be integrated, preferably stablyintegrated, into the genome of the host organism or may remainextra-genomic or extra-chromosomal. Insofar the host organism comprisessaid agent, isolated nucleic acid or construct (vector), it may bedenoted a ‘transgenic’ or ‘transformed’ organism in that regard.Preferably, a host organism expresses or is under suitable conditionscapable of expressing the isolated nucleic acid or vector comprisedtherein, thereby producing the anti-DUX4 and/or anti-DUX4c antisenseagent or RNAi agent encoded thereby. Also contemplated is thus a methodfor producing any one or more anti-DUX4 and/or anti-DUX4c antisenseagent or RNAi agent as taught herein comprising culturing or maintaininga host organism comprising an isolated nucleic acid encoding said agentor an expression construct (expression vector) comprising a nucleic acidencoding said agent, under conditions conducive to expression of saidagent from said isolated nucleic acid or expression construct. Theso-produced agent may be intended to exert its silencing effect in thehost organism expressing it, or may by intended for use elsewhere inwhich case the method may further optionally and preferably comprise atleast partly purifying the agent.

As well encompassed is a progeny of the host cell or host organism astaught herein. Particularly intended is progeny comprising theintroduced agent, or isolated nucleic acid encoding the agent, or aconstruct (vector) comprising a nucleic acid encoding the agent, orcomprising a replicated copy of said nucleic acid or construct (vector),i.e., progeny transgenic or transformed with regard to said nucleic acidor construct.

Also intended are compositions and formulations comprising any one ormore anti-DUX4 and/or anti-DUX4c antisense agent or RNAi agent as taughtherein, or an isolated nucleic acid encoding such an agent, arecombinant construct (vector) (preferably an expression construct,expression vector) comprising a nucleic acid encoding such an agent, ora host cell or host organism as taught herein, and one or moreadditional components, such as without limitation one or more solventsand/or one or more pharmaceutically acceptable carriers. Furtherprovided are methods for producing the above compositions orformulations, comprising admixing said agent, isolated nucleic acid,construct (vector), host cell or host organism as taught herein with oneor more additional components.

Particularly intended are pharmaceutical compositions and formulationscomprising any one or more anti-DUX4 and/or anti-DUX4c antisense agentor RNAi agent as taught herein, or an isolated nucleic acid encodingsuch an agent, a recombinant construct (vector) (preferably anexpression construct, expression vector) comprising a nucleic acidencoding such an agent, or a host cell or host organism as taughtherein, one or more pharmaceutically acceptable carriers; and methodsfor producing said pharmaceutical compositions and formulations,comprising admixing said agent, isolated nucleic acid, construct(vector), host cell or host organism as taught herein with said one ormore pharmaceutically acceptable carriers.

Further disclosed herein are kits of parts comprising any one or moreanti-DUX4 and/or anti-DUX4c antisense agent or RNAi agent as taughtherein, or an isolated nucleic acid encoding such an agent, arecombinant construct (vector) (preferably an expression construct,expression vector) comprising a nucleic acid encoding such an agent, ora host cell or host organism or progeny thereof as taught herein, orcomposition(s) or formulation(s) comprising any of such. The componentsof the kits may be in various forms, such as, e.g., lyophilised, free insolution or immobilised on a solid phase. They may be, e.g., provided ina multi-well plate or as an array or microarray, or they may be packagedseparately and/or individually. A kit will further typically compriseinstructions for its use. The kits may be advantageously employed invarious applications, such as inter alia in therapeutic, diagnostic,compound-screening and research applications.

Further provided is:

-   -   any one or more anti-DUX4 and/or anti-DUX4c antisense agent or        RNAi agent as taught herein, or an isolated nucleic acid        encoding such an agent, a recombinant construct (vector)        (preferably an expression construct, expression vector)        comprising a nucleic acid encoding such an agent, or a host cell        or host organism or progeny thereof as taught herein, or        composition(s) or formulation(s) comprising any of such, for use        as a medicament; or for use in the treatment of a disease or        condition the treatment of which can benefit from reducing the        expression of double homeobox 4 and/or double homeobox 4c;    -   use of any one or more anti-DUX4 and/or anti-DUX4c antisense        agent or RNAi agent as taught herein, or an isolated nucleic        acid encoding such an agent, a recombinant construct (vector)        (preferably an expression construct, expression vector)        comprising a nucleic acid encoding such an agent, or a host cell        or host organism or progeny thereof as taught herein, or        composition(s) or formulation(s) comprising any of such, for the        manufacture of a medicament for the treatment of a disease or        condition the treatment of which can benefit from reducing the        expression of double homeobox 4 and/or double homeobox 4c; or    -   a method for treating a disease or condition the treatment of        which can benefit from reducing the expression of double        homeobox 4 and/or double homeobox 4c in a subject, comprising        administering to said subject a therapeutically or        prophylactically effective amount of any one or more anti-DUX4        and/or anti-DUX4c antisense agent or RNAi agent as taught        herein, or an isolated nucleic acid encoding such an agent, a        recombinant construct (vector) (preferably an expression        construct, expression vector) comprising a nucleic acid encoding        such an agent, or a host cell or host organism or progeny        thereof as taught herein, or composition(s) or formulation(s)        comprising any of such.

Preferably, the diseases or conditions include ones comprising increasedlevels and/or increased activity of double homeobox 4 and/or doublehomeobox 4c, more preferably the disease or condition isfacioscapulohumeral muscular dystrophy (FSHD). Double homeobox 4 emergesas particularly implicated in the aetiology of FSHD. Anti-DUX4 antisenseand/or RNAi agents and the related or derived reagents are thuspreferred.

It shall be appreciated that the reference herein to “any one or moreanti-DUX4 and/or anti-DUX4c antisense agent or RNAi agent” covers notonly such single agents, but also any combinations of two or more suchagents. Expressly intended are without limitation a combination of twoor more anti-DUX4 and/or anti-DUX4c antisense agents; a combination oftwo or more anti-DUX4 and/or anti-DUX4c RNAi agents; and a combinationof one or more anti-DUX4 and/or anti-DUX4c antisense agent and one ormore anti-DUX4 and/or anti-DUX4c RNAi agent. Agents in a combination oftwo or more agents may be typically provided as separate molecules, ormay otherwise be covalently or non-covalently conjugated to one another,either directly or via a suitable linker or carrier. A non-limitingexample of joined agents includes “weasel” agents of two or moreco-joined antisense oligonucleotides as disclosed in WO 2006/000057, orin Aartsma-Rus et al. 2004 (Am J Hum Genet 74: 83-92).

The above and further aspects and preferred embodiments of the inventionare described in the following sections and in the appended claims. Thesubject matter of appended claims 1 to 28 is hereby specificallyincorporated in this specification.

BRIEF DESCRIPTION OF FIGURES

FIG. 1 illustrates a schematic representation of the DUX4 transcriptsexpressed from an exemplary pathogenic D4Z4 repeat array containing fourD4Z4 units (grey arrows) at the 4q35 locus. Each of the four D4Z4 unitscontains the DUX4 open reading frame (ORF) (white boxes) and atranscription start site (white bended arrows). The repeat array isflanked on its telomeric end by the pLAM region (grey box) which is onlypresent on the 4qA allele uniquely linked to FSHD. The alternative 4qBallele is not linked to FSHD (Lemmers et al. 2004 (Am J Hum Genet 75(6):1124-30)).

FIG. 2 illustrates a scheme of an EcoRI genomic fragment cloned inpGEM7Z and encompassing the 3′portion of the DUX4 ORF and its 3′ UTR.The stop codon of the DUX4 ORF, the pLAM region and the poly-A additionsignal (ATTAAA) are indicated in the upper panel. The lower panelcaptures the mapping of the 3′ mRNA ends and illustrates the location ofintrons 1 and 2. Intron 1 is alternatively spliced. The nucleotidepositions are as shown in the sequence in FIG. 3.

FIG. 3 illustrates the sequence (SEQ ID NO: 1) of an exemplary genomicfragment as schematically set out in FIG. 2, encompassing the 3′ portionof the DUX4 ORF and its 3′ UTR. This particular sequence reproducespositions 12001 to 13080 of the genomic sequence available in the NCBIGenbank database under accession number AF117653 (sequence version no.2, i.e., AF117653.2). In this AF117653 sequence said DUX4 ORF extendsfrom an ATG translation initiation codon at position 10829 (not shown)to the stop codon at positions 12101-12103 (boxed). Exon 1 ends atposition 12111, intron 1 extends from position 12112 to 12247 within theD4Z4 unit (italics), exon 2 extends from position 12248 to 12329 (bold),the last D4Z4 unit ends at position 12329 continuing with the pLAMregion, intron 2 extends from position 12330 to 12684 (larger) (italics)or alternatively 12338-12682 (smaller), and exon 3 extends from position12685 to 12873 (bold).

FIG. 4 illustrates the sequence (SEQ ID NO: 42) of an exemplary DUX4cDNA. The DUX4 ORF, demarcated by the translation initiation codon(bold, boxed) and the stop codon (boxed), and the 5′ UTR upstream of theATG codon correspond to these portions in the exemplary DUX4 cDNAsequence available in Genbank under accession no. NM_(—)033178 (sequenceversion 2, i.e., NM_(—)033178.2). The 3′ UTR downstream of the stopcodon (i.e., starting from position 1576 of SEQ ID NO: 42) is compiledfrom the DUX4 genomic sequence AF117653.2 (see FIG. 3 and legendthereto) and includes the remainder of exon 1, intron 1 (italics), exon2 (bold) and exon 3 (underlined).

FIG. 5 illustrates the sequence (SEQ ID NO: 43) of an exemplary DUX4cDNA. The DUX4 ORF, demarcated by the translation initiation codon(bold, boxed) and the stop codon (boxed), and the 5′ UTR upstream of theATG codon correspond to these portions in the exemplary DUX4 cDNAsequence available in Genbank under accession no. NM_(—)033178 (sequenceversion 2, i.e., NM_(—)033178.2). The 3′ UTR downstream of the stopcodon (i.e., starting from position 1576 of SEQ ID NO: 43) is compiledfrom the DUX4 genomic sequence AF117653.2 (see FIG. 3 and legendthereto) and includes the remainder of exon 1, exon 2 (bold) and exon 3(underlined).

FIG. 6 illustrates the sequence (SEQ ID NO: 50) of an exemplary putativeDUX4c cDNA. This sequence corresponds to positions 727 to 2440 of anexemplary but non-limiting genomic sequence of the DUX4c gene (Genbankaccession no. AY500824, sequence version 1, i.e., AY500824.1). Indicatedare the putative GC-box (underlined) at positions 1-13 of SEQ ID NO: 50(positions 727-739 of AY500824.1), the putative TATA-box variant (doubleunderlined) at positions 48-52 of SEQ ID NO: 50 (positions 774-778 ofAY500824.1), the DUX4c ORF demarcated by the translation initiationcodon (bold, boxed) at positions 192-194 of SEQ ID NO: 50 (positions918-920 of AY500824.1) and the stop codon (boxed) at positions 1314-1316of SEQ ID NO: 50 (positions 2040-2042 of AY500824.1). The 3′ UTR asexperimentally detected extends downstream of the stop codon (i.e.,starting from position 1317 of SEQ ID NO: 50; position 2043 ofAY500824.1) down to position 1714 of SEQ ID NO: 50 (position 2440 ofAY500824.1).

FIG. 7 illustrates the sequence (SEQ ID NO: 51) of an exemplary putativeDUX4c cDNA. This sequence corresponds to positions 727 to 2629 of anexemplary but non-limiting genomic sequence of the DUX4c gene (Genbankaccession no. AY500824, sequence version 1, i.e., AY500824.1). Indicatedare the putative GC-box (underlined) at positions 1-13 of SEQ ID NO: 51(positions 727-739 of AY500824.1), the putative TATA-box variant (doubleunderlined) at positions 48-52 of SEQ ID NO: 51 (positions 774-778 ofAY500824.1), the DUX4c ORF demarcated by the translation initiationcodon (bold, boxed) at positions 192-194 of SEQ ID NO: 51 (positions918-920 of AY500824.1) and the stop codon (boxed) at positions 1314-1316of SEQ ID NO: 51 (positions 2040-2042 of AY500824.1). The 3′ UTR asexperimentally detected in an FSHD patient extends downstream of thestop codon (i.e., starting from position 1317 of SEQ ID NO: 51; position2043 of AY500824.1) down to position 1903 of SEQ ID NO: 51 (position2629 of AY500824.1).

FIG. 8 illustrates the sequence (SEQ ID NO: 52) of an exemplary putativeDUX4c cDNA. This sequence corresponds to predicted DUX4c mRNA asavailable in the Genbank database under accession no. XR_(—)041199(sequences version 2, i.e., XR_(—)041199.2). Indicated are the DUX4c ORFdemarcated by the translation initiation codon (bold, boxed) atpositions 688-670 and the stop codon (boxed) at positions 1810-1812. Thepredicted 3′ UTR extends downstream of the stop codon (i.e., startingfrom position 1813.

FIG. 9 illustrates the inhibitory effect of anti-DUX4 pre-mRNA antisenseoligomers on DUX4 protein expression.

FIGS. 10 and 11 illustrate that antisense oligomer 1524 can exert aspecific inhibitory effect on DUX4 protein expression.

FIG. 12 illustrates that antisense oligomers 1524, 1523 and 1522 canexert a specific inhibitory effect on DUX4 protein expression.

FIGS. 13A, 13B and 14 illustrate evaluation of siRNA targeting DUX4c.

FIG. 15 illustrates evaluation of siRNA targeting DUX4.

FIG. 16 illustrates evaluation of anti-DUX4c and anti-DUX4 siRNAspecificity by Western blot. (A) anti-DUX4 antibody, (B) anti-DUX4cantibody.

FIG. 17 illustrates pLVTH-shRNA expression vector.

FIG. 18 schematically illustrates production of shRNA from an shRNAvector and its subsequence processing to siRNA by Dicer.

FIG. 19 illustrates efficiency and specificity of shRNA vectors inwestern blot.

FIG. 20 illustrates an exemplary sequence of DUX4 protein.

FIG. 21 illustrates an exemplary sequence of DUX4c protein.

FIG. 22 illustrates optimal transfection conditions for FSHD primarymyoblasts.

FIG. 23 illustrates evaluation of siRNA targeting DUX4 in FSHD primarymyoblasts.

FIG. 24 illustrates a schematic representation of the structure of anoligonucleotide chemically modified with a 2′-O-methylatedphosphorothioate backbone.

FIG. 25 illustrates a schematic representation of the structure of anoligonucleotide chemically modified with a phosphorodiamidate morpholinobackbone.

FIG. 26 illustrates exemplary transcripts derived from one or more D4Z4units and comprising the pLAM region or not. The upper panelschematically shows genomic fragments of a D4Z4 unit and the pLAMregion. The DUX4 ORF is represented in black with the two homeoboxregions in grey. The positions of the different introns are indicated(dark grey boxes). The pLAM region encompasses an intron (dark grey box)and the poly-A signal (ATTAAA). The lower panels illustrate the locationof introns 1, 2, 2a, 1 bis and 2a bis. The first transcript published(Dixit et al., supra) begins in the last D4Z4 unit with alternativesplicing of intron 1 in the D4Z4 sequence, then extending into the pLAMregion where intron 2 is always spliced out, and ending 6 to 16 bp afterthe poly-A signal. We found a second transcript (Coppée et al.,unpublished) that begins in a D4Z4 unit (adjacent or not to the lastunit) that has the same intron 1 as reported above. The transcriptcontinues in the adjacent D4Z4 unit where another intron is found thatis named either 2a if the splice acceptor site is in the D4Z4 unit or 2abis if this splice acceptor site is in the pLAM region. No poly-Asignals were reported at proximity. Snider et al., supra found a DUX4transcript corresponding to those described in Dixit et al. and a DUX4transcript with 2 copies of exon 2.

FIG. 27 illustrates exemplary genomic sequence of the DUX4 transcriptsof FIG. 26. Snider et al. reported a different sequence for thebeginning of the pLAM region that contains the intron 2 donor splicingsite (boxed sequence GGTACC). Sequence comparison revealed that thissequence is identical to those in the beginning of a D4Z4 unitsurrounding the intron 2a splice donor site (Coppée et al.).

FIG. 28 schematically shows the DUX4 gene structure by aligning D4Z4 andpLAM variants. Two adjacent D4Z4 units are represented to scale fromGenBank accession number AF117653.1 (first and second line) as well asthe flanking pLAM region (fourth line). This region differs from thatrepresented in the third line (GenBank accession number U74497.1) by adeletion of a 1609-bp segment (vertical stripes). This pLAM region(third line) is nearly identical to a D4Z4 unit over 1890 bp (greystripes) and diverges in further distal sequences. The 1609-bp deletionin the pLAM region of the fourth line is found in the region nearlyidentical to D4Z4. The DUX4 ORF is represented in black with the twohomeobox regions in grey. The positions of the different introns areindicated (dark grey boxes). The DUX4 mRNA start sites are indicated byblack upward arrows for the 1^(st) mRNA (Dixit et al. 2007) and the2^(nd) mRNA (Coppée et al., unpublished). The DUX4 mRNA ends areindicated by black downwards arrows. Different ends were found: 6 to 16bp downstream from the poly-A signal (Dixit et al., 2007) for the 1^(st)mRNA, and two possible ends (either in D4Z4 or in pLAM) for the 2^(nd)mRNA.

FIGS. 29A and 29B illustrate the efficiency of the antisenseoligonucleotides 1521 (a) and 1523 (b) in decreasing endogenous DUX4mRNA amount in FSHD primary myotubes.

FIG. 30 illustrates the efficiency of anti-DUX4 siRNA3 in decreasingendogenous DUX4 mRNA amount in FSHD primary myotubes.

FIG. 31 schematically shows the position of the antisenseoligonucleotides 2245 and 2250 on the DUX4 genomic sequence fragmentavailable in Genbank under accession no. AF117653 (sequence version 2,i.e., AF117653.2). (see FIG. 3 and legend thereto). This sequencefragment includes intron 1 (italics), exon 2 (bold), exon 3 (italics,bold) and the stop codon of the DUX4 ORF (boxed), antisenseoligonucleotides 2245 (underlined) and 2250 (underlined, bold).

FIG. 32 illustrates the inhibitory effect of the antisense oligomers2245 and 2250 on DUX4 protein expression.

FIG. 33 illustrates optimal concentration of antisense oligomer 2245 forspecific inhibition of DUX4 protein expression.

DETAILED DESCRIPTION OF THE INVENTION

As used herein, the singular forms “a”, “an”, and “the” include bothsingular and plural referents unless the context clearly dictatesotherwise.

The terms “comprising”, “comprises” and “comprised of” as used hereinare synonymous with “including”, “includes” or “containing”, “contains”,and are inclusive or open-ended and do not exclude additional,non-recited members, elements or method steps.

The recitation of numerical ranges by endpoints includes all numbers andfractions subsumed within the respective ranges, as well as the recitedendpoints.

The terms “about” or “approximately” as used herein when referring to ameasurable value such as a parameter, an amount, a temporal duration,and the like, is meant to encompass variations of and from the specifiedvalue, in particular variations of +/−10% or less, preferably +/−5% orless, more preferably +/−1% or less, and still more preferably +/−0.1%or less of and from the specified value, insofar such variations areappropriate to perform in the disclosed invention. It is to beunderstood that the value to which the modifier “about” refers is itselfalso specifically, and preferably, disclosed.

All documents cited in the present specification are hereby incorporatedby reference in their entirety.

Unless otherwise defined, all terms used in disclosing the invention,including technical and scientific terms, have the meaning as commonlyunderstood by one of ordinary skill in the art to which this inventionbelongs. By means of further guidance, term definitions may be includedto better appreciate the teaching of the present invention.

For general methods relating to the invention, reference is made interalia to well-known textbooks, including, e.g., “Molecular Cloning: ALaboratory Manual, 2nd Ed.” (Sambrook et al., 1989), Animal Cell Culture(R. I. Freshney, ed., 1987), the series Methods in Enzymology (AcademicPress), Gene Transfer Vectors for Mammalian Cells (J. M. Miller & M. P.Calos, eds., 1987); “Current Protocols in Molecular Biology and ShortProtocols in Molecular Biology, 3rd Ed.” (F. M. Ausubel et al., eds.,1987 & 1995); Recombinant DNA Methodology II (R. Wu ed., Academic Press1995).

General techniques in cell culture and media uses are outlined interalia in Large Scale Mammalian Cell Culture (Hu et al. 1997. Curr OpinBiotechnol 8: 148); Serum-free Media (K. Kitano. 1991. Biotechnology 17:73); or Large Scale Mammalian Cell Culture (Curr Opin Biotechnol 2: 375,1991).

As used herein, the terms “double homeobox 4” and “DUX4” are synonymousand refer to genes, gene products, nucleic acids, proteins andpolypeptides commonly known under these designations in the art. Theterms encompass such genes, gene products, nucleic acids, proteins andpolypeptides of any organism where found, and particularly of animals,preferably vertebrates, more preferably mammals, including humans andnon-human mammals, even more preferably of humans

The terms particularly encompass such genes, gene products, nucleicacids, proteins and polypeptides with a native sequence, i.e., ones ofwhich the primary sequence is the same as that of DUX4 found in orderived from nature. A skilled person understands that native sequencesof DUX4 may differ between different species due to genetic divergencebetween such species. Moreover, the native sequences of DUX4 may differbetween or within different individuals of the same species due tonormal genetic diversity (genetic variation) or due to mutation within agiven species. Also, the native sequences of DUX4 may differ between oreven within different individuals of the same species due topost-transcriptional or post-translational modifications. Accordingly,all DUX4 sequences found in or derived from nature are considered“native”.

The terms encompass DUX4 genes, gene products, nucleic acids, proteinsand polypeptides when forming a part of a living organism, organ, tissueor cell, when forming a part of a biological sample, as well as when atleast partly isolated from such sources. The terms also encompass genes,gene products, nucleic acids, proteins and polypeptides when produced byrecombinant or synthetic means.

DUX4 gene as intended herein may particularly denote a DUX4 gene presentin the distal-most unit of a D4Z4 array on chromosome 4q35, particularlywherein the DUX4 gene extends into the pLAM region flanking thetelomeric side of the D4Z4 array, more particularly wherein said pLAMregion provides a polyadenylation signal, such as preferably ATTAAA.Such DUX4 gene leads to production of comparably stable mRNA(s) (Dixitet al. 2007, supra).

While additional DUX4 transcripts have been identified that may spanseveral D4Z4 units and may display alternative splicing, and preferablyalso comprise the pLAM region (Snider et al. 2009, supra; Coppée et al.,unpublished), DUX4 gene as intended herein may also particularly denotesuch D4Z4-resident transcription units, particularly ones that give riseto a transcript leading to production of comparably stable mRNAcomprising DUX4 sequences, even more particularly wherein the transcriptcomprises the pLAM region, still more particularly wherein said pLAMregion provides a polyadenylation signal, such as preferably ATTAAA.Such DUX4 transcripts and mRNA are schematically illustrated in FIGS. 26and 28 with reference to an exemplary but non-limiting genomic sequenceas shown in FIG. 27.

It shall also be appreciated that the pLAM region may displaypolymorphisms, such as without limitation the presence or absence of a1.6-kb sequence within its intron (Gabriëls et al. 1999, supra; vanDeutekom et al. 2009, supra).

Even more particularly, DUX4 gene as intended herein denotes DUX4 geneas above as present in a pathogenic D4Z4 array associated withfacioscapulohumeral muscular dystrophy (FSHD).

Exemplary DUX4 gene includes without limitation human DUX4 gene havingnucleic acid sequence as annotated under NCBI Genbank(http://www.ncbi.nlm.nih.gov/) accession number AF117653 (sequenceversion no. 2 revised on Nov. 30, 2009, i.e., AF117653.2), moreparticularly the DUX4 gene at positions about 10650 to about 12873 ofAF117653.2, also particularly at positions about 10829 to about 12873 ofAF117653.2.

Exemplary but non-limiting DUX4 cDNA (and respective mRNA) includeswithout limitation human DUX4 cDNA having nucleic acid sequence asannotated under Genbank accession number NM_(—)033178 (sequence version2 revised on Feb. 28, 2010, i.e., NM_(—)033178.2). Further exemplary butnon-limiting DUX4 cDNA (and respective mRNA) include without limitationhuman DUX4 cDNA having nucleic acid sequence as set out in SEQ ID NO: 42(FIG. 4) or SEQ ID NO: 43 (FIG. 5).

Exemplary DUX4 protein or polypeptide includes without limitation humanDUX4 protein or polypeptide having primary amino acid sequence asannotated under Genbank accession no. NP_(—)149418 (sequence version 3revised on Feb. 28, 2010, i.e., NP_(—)149418.3), also reproduced in FIG.20 as SEQ ID NO: 59.

As used herein, the terms “double homeobox 4c” and “DUX4c” aresynonymous and refer to genes, gene products, nucleic acids, proteinsand polypeptides commonly known under these designations in the art. Theterms encompass such genes, gene products, nucleic acids, proteins andpolypeptides of any organism where found, and particularly of animals,preferably vertebrates, more preferably mammals, including humans andnon-human mammals, even more preferably of humans.

The terms particularly encompass such genes, gene products, nucleicacids, proteins and polypeptides with a native sequence, i.e., ones ofwhich the primary sequence is the same as that of DUX4c found in orderived from nature. A skilled person understands that native sequencesof DUX4c may differ between different species due to genetic divergencebetween such species. Moreover, the native sequences of DUX4c may differbetween or within different individuals of the same species due tonormal genetic diversity (genetic variation) or due to mutation within agiven species. Also, the native sequences of DUX4c may differ between oreven within different individuals of the same species due topost-transcriptional or post-translational modifications. Accordingly,all DUX4c sequences found in or derived from nature are considered“native”.

The terms encompass DUX4c genes, gene products, nucleic acids, proteinsand polypeptides when forming a part of a living organism, organ, tissueor cell, when forming a part of a biological sample, as well as when atleast partly isolated from such sources. The terms also encompass genes,gene products, nucleic acids, proteins and polypeptides when produced byrecombinant or synthetic means.

Exemplary DUX4c gene includes without limitation human DUX4c gene havingnucleic acid sequence as annotated under Genbank accession numberAY500824 (sequence version 1 revised on Dec. 1, 2009, i.e., AY500824.1).A further exemplary DUX4c gene includes without limitation human DUX4cgene having nucleic acid sequence as annotated under Genbank accessionnumber NC_(—)000004 range 190940254.190945505, complement (sequenceversion 11 revised on Jun. 10, 2009, i.e., NC_(—)000004.11).

Exemplary but non-limiting DUX4c cDNA (and respective mRNA) includeswithout limitation human DUX4c cDNA having nucleic acid sequence as setout in SEQ ID NO: 50 (FIG. 6) or SEQ ID NO: 51 (FIG. 7). A furtherexemplary but non-limiting DUX4c cDNA (and respective mRNA) includeswithout limitation human DUX4c cDNA having nucleic acid sequence asannotated under Genbank accession no. XR_(—)041199 (sequences version 2revised on Jun. 10, 2009, i.e., XR_(—)041199.2) also reproduced in FIG.8.

Exemplary DUX4c protein or polypeptide includes without limitation humanDUX4c protein or polypeptide having primary amino acid sequence asannotated under Genbank accession no. AAS15569 (sequence version 1revised on Dec. 1, 2009, i.e., AAS15569.1), also reproduced in FIG. 21as SEQ ID NO: 60.

It shall be appreciated that other DUX genes homologous to DUX4 and/orDUX4c are present in and transcribed from the human genome but are notlinked to FSHD. Consequently, antisense and siRNA agents as intendedherein preferably target DUX4 and/or DUX4c genes specifically, i.e.,substantially to the exclusion of other DUX genes. In particular, suchspecific agents may display adequate sequence identity to DUX4 and/orDUX4c sequences but not to said other DUX genes. The particularantisense and siRNA agents as taught herein are highly advantageous inthis respect.

The reference herein to DUX4 and DUX4c genes, gene products, nucleicacids, proteins and polypeptides also encompasses fragments and/orvariants of the respective substances.

The term “fragment” with reference to a protein or polypeptide generallydenotes a N- and/or C-terminally truncated form of a protein orpolypeptide. Preferably, a fragment may comprise at least about 30%,e.g., at least about 50% or at least about 70%, preferably at leastabout 80%, e.g., at least about 85%, more preferably at least about 90%,and yet more preferably at least about 95% or even about 99% of theamino acid sequence length of said protein or polypeptide.

The term “fragment” with reference to a nucleic acid (polynucleotide)generally denotes a 5′- and/or 3′-truncated form of a nucleic acid.Preferably, a fragment may comprise at least about 30%, e.g., at leastabout 50% or at least about 70%, preferably at least about 80%, e.g., atleast about 85%, more preferably at least about 90%, and yet morepreferably at least about 95% or even about 99% of the nucleic acidsequence length of said nucleic acid.

The term “variant” of a given recited nucleic acid (polynucleotide),protein or polypeptide refers to nucleic acids, proteins or polypeptidesthe sequence (i.e., nucleotide sequence or amino acid sequence,respectively) of which is substantially identical (i.e., largely but notwholly identical) to the sequence of said recited nucleic acid, proteinor polypeptide, e.g., at least about 80% identical or at least about 85%identical, e.g., preferably at least about 90% identical, e.g., at least91% identical, 92% identical, more preferably at least about 93%identical, e.g., at least 94% identical, even more preferably at leastabout 95% identical, e.g., at least 96% identical, yet more preferablyat least about 97% identical, e.g., at least 98% identical, and mostpreferably at least 99% identical. Preferably, a variant may displaysuch degrees of identity to a recited nucleic acid, protein orpolypeptide when the whole sequence of the recited nucleic acid, proteinor polypeptide is queried in the sequence alignment (i.e., overallsequence identity).

Also included among fragments and variants of a given recited nucleicacid, protein or polypeptide are fusion products of said nucleic acid,protein or polypeptide with another, usually unrelated, nucleic acid,protein or polypeptide, respectively. Particularly included amongfragments and variants as intended herein are thus fusion genes betweenthe DUX4 or DUX4c gene and other genes, leading to the expression offusion (i.e., chimeric) proteins. More specifically included are suchfusion genes arising through chromosomal rearrangements, even morespecifically wherein said fusion genes and their chimeric proteins causeor contribute to a pathology. Hence, examples of DUX4 or DUX4c fragmentsand variants which are encompassed herein and may benefit from targetingby the antisense or RNAi agents of the present invention include fusionsbetween CIC, a human homolog of Drosophila capicua, and DUX4, as seen inEwing's family tumours (EFTs) (Kawamura-Saito et al. 2006, supra) andpaediatric undifferentiated soft tissue sarcomas (USTS) (Yoshimoto etal. 2009, supra), and fusions between EWSR1 and DUX4, as seen inrhabdomyosarcomas (RMS) (Sirvent et al. 2009, supra). More generally,fusions containing the C-terminal fragment of DUX4 are intended, sincethe resultant chimeric proteins acquire an enhanced transcriptionalactivity, which may lead to tumour formation.

Sequence identity may be determined using suitable algorithms forperforming sequence alignments and determination of sequence identity asknow per se. Exemplary but non-limiting algorithms include those basedon the Basic Local Alignment Search Tool (BLAST) originally described byAltschul et al. 1990 (J Mol Biol 215: 403-10), such as the “Blast 2sequences” algorithm described by Tatusova and Madden 1999 (FEMSMicrobiol Lett 174: 247-250), for example using the published defaultsettings or other suitable settings (such as, e.g., for the BLASTNalgorithm: cost to open a gap=5, cost to extend a gap=2, penalty for amismatch=−2, reward for a match=1, gap x_dropoff=50, expectationvalue=10.0, word size=28; or for the BLASTP algorithm: matrix=Blosum62,cost to open a gap=11, cost to extend a gap=1, expectation value=10.0,word size=3).

In an embodiment, a variant of a given nucleic acid (polynucleotide),protein or polypeptide may be a homologue (e.g., orthologue orparalogue) of said nucleic acid, protein or polypeptide. As used herein,the term “homology” generally denotes structural similarity between twomacromolecules, particularly between two nucleic acids, proteins orpolypeptides, from same or different taxons, wherein said similarity isdue to shared ancestry.

Where the present specification refers to variants and/or fragments ofsubstances such as of antisense or RNAi agents, nucleic acids, proteinsor polypeptides, this particularly denotes variants and/or fragmentswhich are “functional”, i.e., which at least partly retain thebiological activity or intended functionality of the respective agents,nucleic acids, proteins or polypeptides.

By means of an example and not limitation, a functional variant and/orfragment of a DUX4 or DUX4c gene, gene product, nucleic acid, protein orpolypeptide shall at least partly retain the biological activity of DUX4or DUX4c, respectively. For example, such functional variant and/orfragment may retain one or more aspects of the biological activity ofDUX4 or DUX4c, such as, e.g., ability to participate in one or morecellular pathways, ability to regulate transcription of one or moregenes, etc.

By means of an example and not limitation, a functional variant and/orfragment of an anti-DUX4 and/or anti-DUX4c antisense agent or RNAi agentshall at least partly retain the functionality of said agent, i.e., itsability to reduce or abolish the expression of the target molecule suchas DUX4 and/or DUX4c.

Preferably, a functional variant and/or fragment may retain at leastabout 20%, e.g., at least 30%, or at least about 40%, or at least about50%, e.g., at least 60%, more preferably at least about 70%, e.g., atleast 80%, yet more preferably at least about 85%, still more preferablyat least about 90%, and most preferably at least about 95% or even about100% or higher of the intended biological activity or functionalitycompared to the corresponding recited substance such as an agent, gene,gene product, nucleic acid, protein or polypeptide.

The term “nucleic acid” as used herein typically refers to a polymer(preferably a linear polymer) of any length composed essentially ofnucleoside units. A nucleoside unit commonly includes a heterocyclicbase and a sugar group. Heterocyclic bases may include inter alia purineand pyrimidine bases such as adenine (A), guanine (G), cytosine (C),thymine (T) and uracil (U) which are widespread in naturally-occurringnucleic acids, other naturally-occurring bases (e.g., xanthine, inosine,hypoxanthine) as well as chemically or biochemically modified (e.g.,methylated), non-natural or derivatised bases. Exemplary modifiednucleobases include without limitation 5-substituted pyrimidines,6-azapyrimidines and N-2, N-6 and O-6 substituted purines, including2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. Inparticular, 5-methylcytosine substitutions have been shown to increasenucleic acid duplex stability and may be preferred base substitutions infor example antisense agents, even more particularly when combined with2′-O-methoxyethyl sugar modifications. Sugar groups may include interalia pentose (pentofuranose) groups such as preferably ribose and/or2-deoxyribose common in naturally-occurring nucleic acids, or arabinose,2-deoxyarabinose, threose or hexose sugar groups, as well as modified orsubstituted sugar groups (such as without limitation 2′-O-alkylated,e.g., 2′-O-methylated or 2′-O-ethylated sugars such as ribose;2′-O-alkyloxyalkylated, e.g., 2′-O-methoxyethylated sugars such asribose; or 2′-O,4′-C-alkylene-linked, e.g., 2′-O,4′-C-methylene-linkedor 2′-O,4′-C-ethylene-linked sugars such as ribose; 2′-fluoro-arabinose,etc.). Nucleoside units may be linked to one another by any one ofnumerous known inter-nucleoside linkages, including inter aliaphosphodiester linkages common in naturally-occurring nucleic acids, andfurther modified phosphate- or phosphonate-based linkages such asphosphorothioate, alkyl phosphorothioate such as methylphosphorothioate, phosphorodithioate, alkylphosphonate such asmethylphosphonate, alkylphosphonothioate, phosphotriester such asalkylphosphotriester, phosphoramidate, phosphoropiperazidate,phosphoromorpholidate, bridged phosphoramidate, bridged methylenephosphonate, bridged phosphorothioate; and further siloxane, carbonate,sulfamate, carboalkoxy, acetamidate, carbamate such as 3′-N-carbamate,morpholino, borano, thioether, 3′-thioacetal, and sulfoneinternucleoside linkages. Preferably, inter-nucleoside linkages may bephosphate-based linkages including modified phosphate-based linkages,such as more preferably phosphodiester, phosphorothioate orphosphorodithioate linkages or combinations thereof. The term “nucleicacid” also encompasses any other nucleobase containing polymers such asnucleic acid mimetics, including, without limitation, peptide nucleicacids (PNA), peptide nucleic acids with phosphate groups (PHONA), lockednucleic acids (LNA), morpholino phosphorodiamidate-backbone nucleicacids (PMO), cyclohexene nucleic acids (CeNA), tricyclo-DNA (tcDNA), andnucleic acids having backbone sections with alkyl linkers or aminolinkers (see, e.g., Kurreck 2003 (Eur J Biochem 270: 1628-1644)).“Alkyl” as used herein particularly encompasses lower hydrocarbonmoieties, e.g., C1-C4 linear or branched, saturated or unsaturatedhydrocarbon, such as methyl, ethyl, ethenyl, propyl, 1-propenyl,2-propenyl, and isopropyl. Nucleic acids as intended herein may includenaturally occurring nucleosides, modified nucleosides or mixturesthereof. A modified nucleoside may include a modified heterocyclic base,a modified sugar moiety, a modified inter-nucleoside linkage or acombination thereof. The term “nucleic acid” further preferablyencompasses DNA, RNA and DNA/RNA hybrid molecules, specificallyincluding hnRNA, pre-mRNA, mRNA, cDNA, genomic DNA, amplificationproducts, oligonucleotides, and synthetic (e.g. chemically synthesised)DNA, RNA or DNA/RNA hybrids. A nucleic acid can be naturally occurring,e.g., present in or isolated from nature, can be recombinant, i.e.,produced by recombinant DNA technology, and/or can be, partly orentirely, chemically or biochemically synthesised. A “nucleic acid” canbe double-stranded, partly double stranded, or single-stranded. Wheresingle-stranded, the nucleic acid can be the sense strand or theantisense strand. In addition, nucleic acid can be circular or linear.

Nucleic acids and particularly antisense oligonucleotides or RNAi agentsmay be herein denoted as comprising uracil (U) bases. It shall beappreciated that U may be optionally substituted by thymine (T) in (atleast some) such nucleic acids and agents. For example, as 2′-O-methylphosphorothioate antisense oligonucleotides are more ‘RNA-like’, U maybe used and denoted in such molecules. With other antisense chemistries,such as peptide nucleic acids or morpholino backbones, T bases may bepreferably denoted and used.

The term “oligonucleotide” as used herein refers to a nucleic acid(including nucleic acid analogues and mimetics) oligomer or polymer asdefined herein. Preferably, an oligonucleotide, such as moreparticularly an antisense oligonucleotide, is (substantially)single-stranded. Oligonucleotides as intended herein may be preferablybetween about 10 and about 100 nucleoside units (i.e., nucleotides ornucleotide analogues) in length, preferably between about 15 and about50, more preferably between about 20 and about 40, also preferablybetween about 20 and about 30. Preferably, oligonucleotides as intendedherein may comprise one or more or all non-naturally occurringheterocyclic bases and/or one or more or all non-naturally occurringsugar groups and/or one or more or all non-naturally occurringinter-nucleoside linkages, the inclusion of which may improve propertiessuch as, for example, enhanced cellular uptake, increased stability inthe presence of nucleases and increased hybridization affinity,increased tolerance for mismatches, etc. Further, oligonucleotides asintended herein may be configured to not activate RNAse H, accordancewith known techniques (see, e.g., U.S. Pat. No. 5,149,797).

Antisense agents such as oligonucleotides as taught herein may befurther conjugated (e.g., covalently or non-covalently, directly or viaa suitable linker) to one or more moieties or conjugates that enhancethe activity, cellular distribution or cellular uptake of theoligonucleotide. Such moieties include but are not limited to lipidmoieties such as a cholesterol moiety, cholic acid, a thioether, e.g.,hexyl-S-tritylthiol, a thiocholesterol, an aliphatic chain, e.g.,dodecandiol or undecyl residues, a phospholipid, e.g.,di-hexadecyl-rac-glycerol or triethylammonium1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, a polyamine or apolyethylene glycol chain, or adamantane acetic acid, a palmityl moiety,or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety.

It is not necessary for all positions in a given agent to be uniformlymodified, and in fact more than one of the aforementioned modificationsmay be incorporated in a single agent or even at a single nucleosidewithin an oligonucleotide. Further included are antisense compounds thatare chimeric compounds. “Chimeric” antisense compounds or “chimeras” areantisense molecules, particularly oligonucleotides, which contain two ormore chemically distinct regions, each made up of at least one monomerunit, i.e., a nucleotide in the case of an oligonucleotide compound.These oligonucleotides typically contain at least one region wherein theoligonucleotide is modified so as to confer upon the increasedresistance to nuclease degradation, increased cellular uptake, and anadditional region for increased binding affinity for the target nucleicacid.

The term “antisense” generally refers to an agent (e.g., anoligonucleotide) configured to specifically anneal with (hybridise to) agiven sequence in a target nucleic acid, such as for example in a targetDNA, hnRNA, pre-mRNA or mRNA, and typically comprises, consistessentially of or consist of a nucleic acid sequence that iscomplementary or substantially complementary to said target nucleic acidsequence. Antisense agents suitable for use herein may typically becapable of annealing with (hybridising to) the respective target nucleicacid sequences at high stringency conditions, and capable of hybridisingspecifically to the target under physiological conditions.

The terms “complementary” or “complementarity” as used herein withreference to nucleic acids, refer to the normal binding ofsingle-stranded nucleic acids under permissive salt (ionic strength) andtemperature conditions by base pairing, preferably Watson-Crick basepairing. By means of example, complementary Watson-Crick base pairingoccurs between the bases A and T, A and U or G and C. For example, thesequence 5′-A-G-U-3′ is complementary to sequence 5′-A-C-U-3′.

The term “bind” or “binding” as used herein preferably refers tospecific binding, i.e., where an agent binds to (anneals with) one ormore targets of interest, such as to one or more pre-mRNA molecules orfragments or variants thereof, substantially to the exclusion of othermolecules which are random or unrelated, and optionally substantially tothe exclusion of other molecules that are structurally related. Bindingof an agent to a target may be evaluated inter alia using conventionalinteraction-querying methods, such as in silico sequence analysis ornucleic acid hybridisation experiments, e.g., to verify specifichybridisation, e.g., under high stringency conditions.

Specific binding does not necessarily require that an agent bindsexclusively to its intended target(s). For example, an agent may be saidto specifically bind to a given pre-mRNA of interest or fragments orvariants thereof if its affinity for such intended target(s) under theconditions of binding is at least about 2-fold greater, preferably atleast about 5-fold greater, more preferably at least about 10-foldgreater, yet more preferably at least about 25-fold greater, still morepreferably at least about 50-fold greater, and even more preferably atleast about 100-fold or at least about 1000-fold or more greater, thanits affinity for a non-target molecule, such as non-target other DUXgenes.

The sequence of an antisense agent need not be 100% complementary tothat of its target sequence to bind or hybridise specifically with thelatter. An antisense agent may be said to be specifically hybridisablewhen binding of the agent to a target nucleic acid molecule interfereswith the normal function of the target nucleic acid such as to attain anintended outcome (e.g., loss of utility), and there is a sufficientdegree of complementarity to avoid non-specific binding of the antisenseagent to non-target sequences under conditions in which specific bindingis desired, i.e., under physiological conditions in the case of in vivoassays or therapeutic treatment, and in the case of in vitro assays,under conditions in which the assays are performed. Thus, “specificallyhybridisable” and “complementary” may indicate a sufficient degree ofcomplementarity or precise pairing such that stable and specific bindingoccurs between an antisense agent and a nucleic acid target. Agents asintended herein preferably specifically bind to the desired DUX4 and/orDUX4c targets substantially to the exclusion of other DUX genes.

Preferably, to ensure specificity of antisense agents towards thedesired DUX4 and/or DUX4c targets over unrelated molecules, such as overother DUX genes, the sequence of said antisense agents may be at leastabout 80% identical, preferably at least about 90% identical, morepreferably at least about 95% identical, such as, e.g., about 96%, about97%, about 98%, about 99% and up to 100% identical to the respectivetarget DUX4 and/or DUX4c sequence.

The term “reduce” generally denotes a qualitative and/or quantitativealteration, change or variation leading to decrease of that which isbeing reduced (e.g., production and/or level of a given protein). Theterm covers any extent of such reduction. For example, where reductioneffects a determinable or measurable variable, then such reduction mayencompass a decrease in the value of said variable by at least about10%, e.g., by at least about 20%, by at least about 30%, e.g., by atleast about 40%, by at least about 50%, e.g., by at least about 60%, byat least about 70%, e.g., by at least about 80%, by at least about 90%,e.g., by at least about 95%, such as by at least about 96%, 97%, 98%,99% or even by 100% (abolishment), compared to a reference situationwithout said reduction. Preferably, reduction of the production and/orlevel of intended target(s) may be specific or selective, i.e., theproduction and/or level of the intended target(s) may be modulatedwithout substantially altering the production and/or level of random,unrelated targets.

Agents such as antisense or RNAi agents as taught herein may withoutlimitation reduce or abolish the production and/or level of DUX4 and/orDUX4c pre-mRNA and/or mRNA, whereby such agents may be capable ofreducing or abolishing the production of DUX4 and/or DUX4c proteins.

Reference to the “level” of a target may preferably encompass thequantity and/or the availability (e.g., availability for performing itsbiological activity) of the target, e.g., within a cell, tissue, organor an organism.

The terms “splicing”, “splicing of a gene” and similar as used hereinare synonymous and have their art-established meaning. By means ofadditional explanation, splicing denotes the process and means ofremoving intervening sequences (introns) from pre-mRNA in the process ofproducing mature mRNA. The reference to splicing particularly aims atnative splicing such as occurs under normal physiological conditions.The terms “pre-mRNA” and “transcript” are used herein to denote RNAspecies that precede mature mRNA, such as in particular a primary RNAtranscript and any partially processed forms thereof. Sequence elementsrequired for splicing refer particularly to cis elements in the sequenceof pre-mRNA which direct the cellular splicing machinery (spliceosome)towards correct and precise removal of introns from the pre-mRNA.Sequence elements involved in splicing are generally known per se andcan be further determined by known techniques including inter aliamutation or deletion analysis. By means of further explanation, “splicedonor site” or “5′ splice site” generally refer to a conserved sequenceimmediately adjacent to an exon-intron boundary at the 5′ end of anintron. Commonly, a splice donor site may contain a dinucleotide GU, andmay involve a consensus sequence of about 8 bases at about positions +2to −6. “Splice acceptor site” or “3′ splice site” generally refers to aconserved sequence immediately adjacent to an intron-exon boundary atthe 3′ end of an intron. Commonly, a splice acceptor site may contain adinucleotide AG, and may involve a consensus sequence of about 16 basesat about positions −14 to +2 (see, e.g., FIG. 1 of WO 2006/00057 forillustrative consensus sequences of splice donor and splice acceptorsites).

The terms “polyadenylation”, “polyadenylation of a gene” and similar areused interchangeably herein and have their art-established meaning. Bymeans of additional explanation, polyadenylation denotes the process andmeans of adding a polyadenylic acid (poly(A)) tail, i.e., multipleadenosine monophosphates, to an RNA molecule. In particular,polyadenylation may denote the process and means of adding a poly(A)tail to a pre-mRNA molecule, in the process of producing mature mRNA.The reference to polyadenylation particularly aims at nativepolyadenylation such as occurs under normal physiological conditions.

Sequence elements required for polyadenylation refer particularly to ciselements in the sequence of pre-mRNA which the cellular polyadenylationmachinery recognises such as to which it binds, such as for example thepolyadenylation signal. These sequence such as the polyadenylationsignal may vary between groups of eukaryotes. For example, in humans thepolyadenylation signal sequence may typically be AATAAA (i.e., AAUAAA inRNA such as pre-mRNA), but variants of it exist, such as ATTAAA.

The term “cell-penetrating peptide” or “CPP” generally refers topeptides capable of entering into cells. This ability can be exploitedfor the delivery of agents as disclosed herein to cells. Exemplary butnon-limiting CPP include HIV-1 Tat-derived CPP (see, e.g., Frankel etal. 1988 (Science 240: 70-73)); Antennapedia peptides or penetratins(see, e.g., Derossi et al. 1994 (J Biol Chem 269: 10444-10450));peptides derived from HSV-1 VP22 (see, e.g., Aints et al. 2001 (GeneTher 8: 1051-1056)); transportans (see, e.g., Pooga et al. 1998 (FASEB J12: 67-77)); protegrin 1 (PG-1) anti-microbial peptide SynB (Kokryakovet al. 1993 (FEBS Lett 327: 231-236)); model amphipathic (MAP) peptides(see, e.g., Oehlke et al. 1998 (Biochim Biophys Acta 1414: 127-139));signal sequence-based cell-penetrating peptides (NLS) (see, e.g., Lin etal. 1995 (J Biol Chem 270: 14255-14258)); hydrophobic membranetranslocating sequence (MTS) peptides (see, e.g., Lin et al. 1995,supra); and polyarginine, oligoarginine and arginine-rich peptides (see,e.g., Futaki et al. 2001 (J Biol Chem 276: 5836-5840)). The carrierpeptides that have been derived from these proteins show little sequencehomology with each other, but are all highly cationic and arginine orlysine rich.

CPP can be of any length. For example CPP may be less than or equal to500, 250, 150, 100, 50, 25, 10 or 6 amino acids in length. For exampleCPP may be greater than or equal to 4, 5, 6, 10, 25, 50, 100, 150 or 250amino acids in length. Preferably, a CPP may be between 4 and 25 aminoacids in length. The suitable length and design of the CPP will beeasily determined by those skilled in the art. As a general reference onCPPs can serve inter alia “Cell penetrating peptides: processes andapplications” (ed. Ulo Langel, 1st ed., CRC Press 2002); Advanced DrugDelivery Reviews 57: 489-660 (2005); Dietz & Bahr 2004 (Moll CellNeurosci 27: 85-131)).

An agent as disclosed herein may be conjugated with a CPP directly orindirectly, e.g., by means of a suitable linker, such as withoutlimitation a PEG-based linker “RNA interference” or “RNAi” technology isknown in the art, and refers generally to the process and means ofsequence-specific post-transcriptional gene silencing mediatedparticularly by short interfering nucleic acids (siNA). For teaching onRNAi molecules and design thereof, see inter alia Elbashir et al. 2001(Nature 411: 494-501), Reynolds et al. 2004 (Nat Biotechnol 22: 326-30),http://rnaidesigner.invitrogen.com/rnaiexpress, Wang & Mu 2004(Bioinformatics 20: 1818-20), Yuan et al. 2004 (Nucleic Acids Res 32(WebServer issue): W130-4), by M Sohail 2004 (“Gene Silencing by RNAInterference: Technology and Application”, 1^(st) ed., CRC, ISBN0849321417), U Schepers 2005 (“RNA Interference in Practice: Principles,Basics, and Methods for Gene Silencing in C. elegans, Drosophila, andMammals”, 1^(st) ed., Wiley-VCH, ISBN 3527310207), and DR Engelke & J JRossi 2005 (“Methods in Enzymology, Volume 392: RNA Interference”,1^(st) ed., Academic Press, ISBN 0121827976).

An RNAi agent typically comprises, consists essentially of or consistsof a double-stranded portion or region (notwithstanding the optional andpotentially preferred presence of single-stranded overhangs) of annealedcomplementary strands, one of which has a sequence corresponding to atarget nucleotide sequence (hence, to at least a portion of an mRNA) ofthe target gene to be down-regulated. The other strand of the RNAi agentis complementary to said target nucleotide sequence.

Whereas the sequence of an RNAi agent need not be completely identicalto a target sequence to be down-regulated, the number of mismatchesbetween a target sequence and a nucleotide sequence of the RNAi agent ispreferably no more than 1 in 5 bases, or 1 in 10 bases, or 1 in 20bases, or 1 in 50 bases.

Preferably, to ensure specificity of RNAi agents towards the desiredDUX4 and/or DUX4c targets over unrelated molecules, such as over otherDUX genes, the sequence of said RNAi agents may be at least about 80%identical, preferably at least about 90% identical, more preferably atleast about 95% identical, such as, e.g., about 96%, about 97%, about98%, about 99% and up to 100% identical to the respective target DUX4and/or DUX4c sequence.

An RNAi agent may be formed by separate sense and antisense strands or,alternatively, by a common strand providing for fold-back stem-loop orhairpin design where the two annealed strands of an RNAi agent arecovalently linked.

An siRNA molecule may be typically produced, e.g., synthesised, as adouble stranded molecule of separate, substantially complementarystrands, wherein each strand is about 18 to about 35 bases long,preferably about 19 to about 30 bases, more preferably about 20 to about25 bases and even more preferably about 21 to about 23 bases.

shRNA is in the form of a hairpin structure. shRNA can be synthesizedexogenously or can be formed by transcribing from RNA polymerase IIIpromoters in vivo. Preferably, shRNAs can be engineered in host cells ororganisms to ensure continuous and stable suppression of a desired gene.It is known that siRNA can be produced by processing a hairpin RNA incells.

RNAi agents as intended herein may include any modifications as set outherein for nucleic acids and oligonucleotides, in order to improve theirtherapeutic properties.

In embodiments, at least one strand of an RNAi molecules may have a 3′overhang from about 1 to about 6 bases in length, e.g., from 2 to 4bases, more preferably from 1 to 3 bases. For example, one strand mayhave a 3′ overhang and the other strand may be either blunt-ended or mayalso have a 3′ overhang. The length of the overhangs may be the same ordifferent for each strand. The 3′ overhangs can be stabilised againstdegradation. For example, the RNA may be stabilised by including purinenucleotides, such as A or G nucleotides. Alternatively, substitution ofpyrimidine nucleotides by modified analogues, e.g., substitution of U 3′overhangs by 2′-deoxythymidine is tolerated and does not affect theefficiency of RNAi.

An exemplary but non-limiting siRNA molecule may by characterized by anyone or more, and preferably by all of the following criteria:

-   -   at least about 80% sequence identity, more preferably at least        about 90% or at least about 95% or at least about 97% sequence        identity to target mRNA, e.g., DUX4 and/or DUX4c mRNA;    -   having a sequence which targets an area of the target gene        present in mature mRNA (e.g., an exon or alternatively spliced        intron);    -   showing a preference for targeting the 3′ end of the target        gene.

The exemplary siRNA may be further characterised by one or more or allof the following criteria:

-   -   having a double-stranded nucleic acid length of between 16 to 30        bases and preferably of between 18 to 23 bases, and preferably        of 19 nucleotides;    -   having GC content between about 30 and about 50%    -   having a TT(T) sequence at 3′ end;    -   showing no secondary structure when adopting the duplex form;    -   having a Tm (melting temperature) of lower than 20° C.    -   having the nucleotides indicated here below in the sequence of        the nucleotides, wherein “h” is A, C, T/U but not G; wherein “d”        is A, G, T/U but not C, and wherein “w” is A or T/U, but not G        or C:

— — 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 — — mRNA P′5 A A A Uh w 3′-OH si-ASense OH-3′ T T U A d w 5′-P si-Sense P-5′ A U h w T T3′-OH

Production of agents intended herein, such as antisense agents and RNAiagents, can be carried out by any processes known in the art, such asinter alfa partly or entirely by chemical synthesis (e.g., routinelyknown solid phase synthesis; an exemplary an non-limiting method forsynthesising oligonucleotides on a modified solid support is describedin U.S. Pat. No. 4,458,066; in another example, diethyl-phosphoramiditesare used as starting materials and may be synthesised as described byBeaucage et al. 1981 (Tetrahedron Letters 22: 1859-1862)), or partly orentirely by biochemical (enzymatic) synthesis, e.g., by in vitrotranscription from a nucleic acid construct (template) using a suitablepolymerase such as a T7 or SP6 RNA polymerase, or by recombinant nucleicacid techniques, e.g., expression from a vector in a host cell or hostorganism. Nucleotide analogues can be introduced by in vitro chemical orbiochemical synthesis. In an embodiment, the antisense agents of theinvention are synthesised in vitro and do not include antisensecompositions of biological origin, or genetic vector constructs designedto direct the in vivo synthesis of antisense molecules.

The term “isolated” with reference to a particular component (such asfor instance a nucleic acid) generally denotes that such componentexists in separation from—for example, has been separated from orprepared and/or maintained in separation from—one or more othercomponents of its natural environment. For instance, an isolated humanor animal nucleic acid may exist in separation from a human or animalbody where it naturally occurs.

The term “isolated” as used herein may preferably also encompass thequalifier “purified”. By means of example, the term “purified” withreference to a substance (e.g., an agent or a nucleic acid) does notrequire absolute purity. Instead, it denotes that such substances are ina discrete environment in which their abundance (conveniently expressedin terms of mass or weight or concentration) relative to other relevantsubstances is greater than in a biological sample. A discreteenvironment denotes a single medium, such as for example a singlesolution, gel, precipitate, lyophilisate, etc. Purified substances maybe obtained by known methods including, for example, laboratory orrecombinant synthesis, chromatography, preparative electrophoresis,centrifugation, precipitation, affinity purification, etc.

By means of example and not limitation, purified nucleic acids(including NA-based or NA-comprising agents) may preferably constituteby weight ≧about 10%, more preferably ≧about 50%, such as ≧about 60%,yet more preferably ≧about 70%, such as ≧about 80%, and still morepreferably ≧about 90%, such as ≧about 95%, ≧about 96%, ≧about 97%,≧about 98%, ≧about 99% or even 100%, of the nucleic acid content of thediscrete environment. For example, purity of a nucleic acid may bedetermined by measuring absorbance A₂₆₀/A₂₈₀. Also, an isolated nucleicacid may be purified to homogeneity as determined by agarose- orpolyacrylamide-gel electrophoresis and ethidium bromide or similarstaining

By “encoding” is particularly meant that a nucleic acid sequence orpart(s) thereof corresponds to another nucleic acid sequence in atemplate—transcription product (e.g., RNA or RNA analogue) relationship,or corresponds, by virtue of the genetic code of an organism inquestion, to a particular amino acid sequence, e.g., the amino acidsequence of one or more desired proteins or polypeptides.

Preferably, a nucleic acid encoding one or more proteins or polypeptidesmay comprise an open reading frame (ORF) encoding said protein orpolypeptide. An “open reading frame” or “ORF” refers to a succession ofcoding nucleotide triplets (codons) starting with a translationinitiation codon and closing with a translation termination codon knownper se, and not containing any internal in-frame translation terminationcodon, and potentially capable of encoding a protein or polypeptide.Hence, the term may be synonymous with “coding sequence” as used in theart.

Expression of transcription products or proteins and polypeptides can beachieved through operably linking nucleic acid sequences or ORFsencoding the intended transcription products or proteins andpolypeptides with regulatory sequences allowing for expression of thenucleic acids or ORFs, e.g., in vitro, in a host cell, host organ and/orhost organism. Such expression may be achieved, e.g., under suitable(culture) conditions or upon addition of inducers (e.g., where inducibleregulatory sequences are used).

An “operable linkage” is a linkage in which regulatory sequences andsequences sought to be expressed are connected in such a way as topermit said expression. For example, sequences, such as, e.g., apromoter and an ORF, may be said to be operably linked if the nature ofthe linkage between said sequences does not: (1) result in theintroduction of a frame-shift mutation, (2) interfere with the abilityof the promoter to direct the transcription of the ORF, (3) interferewith the ability of the ORF to be transcribed from the promotersequence.

The precise nature of regulatory sequences or elements required forexpression may vary between expression environments, but may typicallyinclude a promoter and a transcription terminator, and optionally anenhancer, as known per se.

The term “vector” generally refers to a nucleic acid molecule, typicallyDNA, to which nucleic acid segments may be inserted and cloned, i.e.,propagated. Hence, a vector will typically contain one or more uniquerestriction sites, and may be capable of autonomous replication in adefined host or vehicle organism such that the cloned sequence isreproducible. Vectors may include, without limitation, plasmids,phagemids, bacteriophages, bacteriophage-derived vectors, PAC, BAC,linear nucleic acids, e.g., linear DNA, viral vectors, etc., asappropriate. Expression vectors are generally configured to allow forand/or effect the expression of nucleic acids or ORFs introduced theretoin a desired expression system, e.g., in vitro, in a host cell, hostorgan and/or host organism. For example, expression vectors mayadvantageously comprise suitable regulatory sequences.

Preferred vectors for use herein are viral vectors, which are well knownand include vectors derived from for example, but without limitation,retroviruses, vaccinia viruses, poxviruses, adenoviruses, andadeno-associated viruses (AAV). Such viral vectors may me be engineeredby recombinant techniques as known per se to introduce thereto nucleicacid sequence(s) encoding any one of the antisense or RNAi agentsdisclosed herein.

For example, a retroviral vector may be used herein. Generally,retroviral vectors may comprise the retroviral genomic sequencesencoding components necessary for the integration of the recombinantviral genome (randomly) into the host cell genome and the nucleic acidsequence(s) of interest, such as in particular the nucleic acidsequence(s) encoding any one of the antisense or RNAi agents disclosedherein. Such retroviral vectors may be readily constructed usingstandard recombinant techniques (e.g., Sambrook et al., MolecularCloning: A Laboratory Manual, 2d ed., Cold Spring Harbor LaboratoryPress, 1989) from a wide variety of retroviruses, including for example,B, C, and D type retroviruses as well as spumaviruses and lentiviruses(see RNA Tumor Viruses, Second Edition, Cold Spring Harbor Laboratory,1985).

Recombinant adenoviral vectors may also be contemplated for delivery andexpression of antisense or RNAi agents as disclosed herein in a hostcell. Adenovirus-based viral vectors have the advantage of being capableof infecting non-dividing host cells, but the recombinant viral genomeis not integrated into the host cell genome. For example, a suitableadenoviral vector, a method for constructing a recombinant adenoviralvector thereof, and a method for delivering the recombinant vector intohost cells, are described in Xia H et al. (2002) (Nat. Biotech. 20:1006-1010). Use of recombinant AAV (RAAV) vectors is also contemplatedherein. RAAV vectors can infect both dividing and non-dividing cells andmay incorporate its recombinant viral genome into that of the host cell.RAAV vectors may be generated from a variety of adeno-associatedviruses, including for example, serotypes 1 through 6. Generally, RAAVvectors may comprise, in order, a 5′ adeno-associated virus invertedterminal repeat (ITR), a nucleic acid of interest, such as in particulara nucleic acid sequence encoding any one of the antisense or RNAi agentsdisclosed herein, operatively linked to a sequence which regulates itsexpression in a host cell or host organism, and a 3′ adeno-associatedvirus ITR. In addition, the rAAV vector may preferably have apolyadenylation signal. Suitable RAAV vectors are described inter aliain WO 1994/13788, WO 1993/24641, and in Goyenvalle et al. 2004 (Science306: 1796-1799) where antisense sequences are linked to a modified U7small nuclear RNA.

Other preferred viral vectors for use herein are vectors derived from apox virus such as a vaccinia virus, for example an attenuated vacciniavirus such as Modified Virus Ankara (MVA) or NYVAC, an avipox virus suchas fowl pox virus or canary pox virus.

The terms “host cell” and “host organism” may suitably refer to cells ororganisms encompassing both prokaryotes, such as bacteria, andeukaryotes, such as yeast, fungi, protozoan, plants and animalsContemplated as host cells are inter alia unicellular organisms, such asbacteria (e.g., E. coli, Salmonella tymphimurium, Serratia marcescens,or Bacillus subtilis), yeast (e.g., Saccharomyces cerevisiae or Pichiapastoris), (cultured) plant cells (e.g., from Arabidopsis thaliana orNicotiana tobaccum) and (cultured) animal cells (e.g., vertebrate animalcells, mammalian cells, primate cells, human cells or insect cells).Contemplated as host organisms are inter alia multi-cellular organisms,such as plants and animals, preferably animals, more preferablywarm-blooded animals, even more preferably vertebrate animals, stillmore preferably mammals, yet more preferably primates; particularlycontemplated are such animals and animal categories which are non-human.

The reference to antisense agents and RNAi agents as used herein alsoencompasses any pharmaceutically acceptable salts, esters, or salts ofsuch esters, or any other compound which, upon administration to ananimal including a human, is capable of providing (directly orindirectly) the biologically active metabolite or residue thereof.Accordingly, for example, also encompassed in the disclosure arepro-drugs and pharmaceutically acceptable salts of the compounds of theinvention, pharmaceutically acceptable salts of such pro-drugs, andother bio-equivalents.

The term “pharmaceutically acceptable salts” refers to physiologicallyand pharmaceutically acceptable salts of the agents disclosed herein,wherein said salts retain the desired biological activity of the parentagent and do not impart undesired toxicological effects thereto. Foroligonucleotides, preferred examples of pharmaceutically acceptablesalts include but are not limited to (a) salts formed with cations suchas sodium, potassium, ammonium, magnesium, calcium, polyamines such asspermine and spermidine, etc.; (b) acid addition salts formed withinorganic acids, for example hydrochloric acid, hydrobromic acid,sulfuric acid, phosphoric acid, nitric acid and the like; (c) saltsformed with organic acids such as, for example, acetic acid, oxalicacid, tartaric acid, succinic acid, maleic acid, fumaric acid, gluconicacid, citric acid, malic acid, ascorbic acid, benzoic acid, tannic acid,palmitic acid, alginic acid, polyglutamic acid, naphthalenesulfonicacid, methanesulfonic acid, p-toluenesulfonic acid,naphthalenedisulfonic acid, polygalacturonic acid, and the like; and (d)salts formed from elemental anions such as chlorine, bromine, andiodine.

The various active substances of the present disclosure, such as interalia antisense agents, RNAi agents, vectors and cells as taught hereinor pharmaceutically acceptable derivatives thereof, may be formulatedinto pharmaceutical compositions or formulations with one or morepharmaceutically acceptable carriers/excipients.

The term “pharmaceutically acceptable” as used herein is consistent withthe art and means compatible with the other ingredients of apharmaceutical composition and not deleterious to the recipient thereof.

As used herein, “carrier” or “excipient” includes any and all solvents,diluents, buffers (such as, e.g., neutral buffered saline, phosphatebuffered saline, or optionally Tris-HCl, acetate or phosphate buffers),solubilisers (such as, e.g., Tween 80, Polysorbate 80), colloids,dispersion media, vehicles, fillers, chelating agents (such as, e.g.,EDTA or glutathione), amino acids (such as, e.g., glycine), proteins,disintegrants, binders, lubricants, wetting agents, emulsifiers,sweeteners, colorants, flavourings, aromatisers, thickeners, agents forachieving a depot effect, coatings, antifungal agents, preservatives(such as, e.g., Thimerosal™, benzyl alcohol), antioxidants (such as,e.g., ascorbic acid, sodium metabisulfite), tonicity controlling agents,absorption delaying agents, adjuvants, bulking agents (such as, e.g.,lactose, mannitol) and the like. The use of such media and agents forpharmaceutical active substances is well known in the art. Exceptinsofar as any conventional media or agent is incompatible with theactive substance, its use in the therapeutic compositions may becontemplated. Suitable pharmaceutical carriers are described inter aliain Remington's Pharmaceutical Sciences, 18th ed., Mack Publishing Co.,Easton, Pa. (1990).

Illustrative, non-limiting carriers for use in formulating thepharmaceutical compositions include, for example, oil-in-water orwater-in-oil emulsions, aqueous compositions with or without inclusionof organic co-solvents suitable for intravenous (IV) use, liposomes orsurfactant-containing vesicles, particulate preparations with polymericcompounds such as inter alia polylactic acid or polyglycolic acid,microspheres, microbeads and microsomes, powders, tablets, capsules,suppositories, aqueous suspensions, aerosols, and other carriersapparent to one of ordinary skill in the art.

Pharmaceutical carriers may comprise sterile liquids, such as water andoils, including those of petroleum, animal, vegetable or syntheticorigin, such as peanut oil, soybean oil, mineral oil, sesame oil and thelike.

Pharmaceutical compositions of the invention may be formulated foressentially any route of administration, such as without limitation,oral administration (such as, e.g., oral ingestion or inhalation),intranasal administration (such as, e.g., intranasal inhalation orintranasal mucosal application), pulmonary (such as, e.g., by inhalationor insufflation of powders or aerosols), parenteral administration (suchas, e.g., subcutaneous, intravenous, intra-arterial, intramuscular,intraperitoneal or intrasternal injection or infusion, or intracranial,e.g., intrathecal or intraventricular administration), epidermal andtransdermal, or transmucosal (such as, e.g., oral, sublingual,intranasal) administration, topical administration (including inter aliaophthalmic administration), rectal, vaginal or intra-trachealinstillation, and the like. In this way, the therapeutic effectsattainable by the methods and compositions of the invention can be, forexample, systemic, local, tissue-specific, etc., depending of thespecific needs of a given application of the invention. Oligonucleotideswith at least one 2′-O-methoxyethyl modification are believed to beparticularly useful for oral administration.

For example, for oral administration, pharmaceutical compositions may beformulated in the form of pills, tablets, lacquered tablets, coated(e.g., sugar-coated) tablets, granules, hard and soft gelatin capsules,aqueous, alcoholic or oily solutions, syrups, emulsions or suspensions.In an example, without limitation, preparation of oral dosage forms maybe is suitably accomplished by uniformly and intimately blendingtogether a suitable amount of the active compound in the form of apowder, optionally also including finely divided one or more solidcarrier, and formulating the blend in a pill, tablet or a capsule.Exemplary but non-limiting solid carriers include calcium phosphate,magnesium stearate, talc, sugars (such as, e.g., glucose, mannose,lactose or sucrose), sugar alcohols (such as, e.g., mannitol), dextrin,starch, gelatin, cellulose, polyvinylpyrrolidine, low melting waxes andion exchange resins. Compressed tablets containing the pharmaceuticalcomposition can be prepared by uniformly and intimately mixing theactive ingredient with a solid carrier such as described above toprovide a mixture having the necessary compression properties, and thencompacting the mixture in a suitable machine to the shape and sizedesired. Moulded tablets maybe made by moulding in a suitable machine, amixture of powdered compound moistened with an inert liquid diluent.Suitable carriers for soft gelatin capsules and suppositories are, forexample, fats, waxes, semisolid and liquid polyols, natural or hardenedoils, etc.

For example, for oral or nasal aerosol or inhalation administration,pharmaceutical compositions may be formulated with illustrativecarriers, such as, e.g., as in solution with saline, polyethylene glycolor glycols, DPPC, methylcellulose, or in mixture with powdereddispersing agents, further employing benzyl alcohol or other suitablepreservatives, absorption promoters to enhance bioavailability,fluorocarbons, and/or other solubilising or dispersing agents known inthe art. Suitable pharmaceutical formulations for administration in theform of aerosols or sprays are, for example, solutions, suspensions oremulsions of the compounds of the invention or their physiologicallytolerable salts in a pharmaceutically acceptable solvent, such asethanol or water, or a mixture of such solvents. If required, theformulation can also additionally contain other pharmaceuticalauxiliaries such as surfactants, emulsifiers and stabilizers as well asa propellant. Illustratively, delivery may be by use of a single-usedelivery device, a mist nebuliser, a breath-activated powder inhaler, anaerosol metered-dose inhaler (MDI) or any other of the numerousnebuliser delivery devices available in the art. Additionally, misttents or direct administration through endotracheal tubes may also beused.

Examples of carriers for administration via mucosal surfaces depend uponthe particular route, e.g., oral, sublingual, intranasal, etc. Whenadministered orally, illustrative examples include pharmaceutical gradesof mannitol, starch, lactose, magnesium stearate, sodium saccharide,cellulose, magnesium carbonate and the like, with mannitol beingpreferred. When administered intranasally, illustrative examples includepolyethylene glycol, phospholipids, glycols and glycolipids, sucrose,and/or methylcellulose, powder suspensions with or without bulkingagents such as lactose and preservatives such as benzalkonium chloride,EDTA. In a particularly illustrative embodiment, the phospholipid 1,2dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) is used as an isotonicaqueous carrier at about 0.01-0.2% for intranasal administration of thecompound of the subject invention at a concentration of about 0.1 to 3.0mg/ml.

For example, for parenteral administration, pharmaceutical compositionsmay be advantageously formulated as solutions, suspensions or emulsionswith suitable solvents, diluents, solubilisers or emulsifiers, etc.Suitable solvents are, without limitation, water, physiological salinesolution or alcohols, e.g. ethanol, propanol, glycerol, in addition alsosugar solutions such as glucose, invert sugar, sucrose or mannitolsolutions, or alternatively mixtures of the various solvents mentioned.The injectable solutions or suspensions may be formulated according toknown art, using suitable non-toxic, parenterally-acceptable diluents orsolvents, such as mannitol, 1,3-butanediol, water, Ringer's solution orisotonic sodium chloride solution, or suitable dispersing or wetting andsuspending agents, such as sterile, bland, fixed oils, includingsynthetic mono- or diglycerides, and fatty acids, including oleic acid.The compounds and pharmaceutically acceptable salts thereof of theinvention can also be lyophilised and the lyophilisates obtained used,for example, for the production of injection or infusion preparations.For example, one illustrative example of a carrier for intravenous useincludes a mixture of 10% USP ethanol, 40% USP propylene glycol orpolyethylene glycol 600 and the balance USP Water for Injection (WFI).Other illustrative carriers for intravenous use include 10% USP ethanoland USP WFI; 0.01-0.1% triethanolamine in USP WFI; or 0.01-0.2%dipalmitoyl diphosphatidylcholine in USP WFI; and 1-10% squalene orparenteral vegetable oil-in-water emulsion. Water or saline solutionsand aqueous dextrose and glycerol solutions may be preferably employedas carriers, particularly for injectable solutions. Illustrativeexamples of carriers for subcutaneous or intramuscular use includephosphate buffered saline (PBS) solution, 5% dextrose in WFI and0.01-0.1% triethanolamine in 5% dextrose or 0.9% sodium chloride in USPWFI, or a 1 to 2 or 1 to 4 mixture of 10% USP ethanol, 40% propyleneglycol and the balance an acceptable isotonic solution such as 5%dextrose or 0.9% sodium chloride; or 0.01-0.2% dipalmitoyldiphosphatidylcholine in USP WFI and 1 to 10% squalene or parenteralvegetable oil-in-water emulsions.

Where aqueous formulations are preferred, such may comprise one or moresurfactants. For example, the composition can be in the form of amicellar dispersion comprising at least one suitable surfactant, e.g., aphospholipid surfactant. Illustrative examples of phospholipids includediacyl phosphatidyl glycerols, such as dimyristoyl phosphatidyl glycerol(DPMG), dipalmitoyl phosphatidyl glycerol (DPPG), and distearoylphosphatidyl glycerol (DSPG), diacyl phosphatidyl cholines, such asdimyristoyl phosphatidylcholine (DPMC), dipalmitoyl phosphatidylcholine(DPPC), and distearoyl phosphatidylcholine (DSPC); diacyl phosphatidicacids, such as dimyristoyl phosphatidic acid (DPMA), dipahnitoylphosphatidic acid (DPPA), and distearoyl phosphatidic acid (DSPA); anddiacyl phosphatidyl ethanolamines such as dimyristoyl phosphatidylethanolamine (DPME), dipalmitoyl phosphatidyl ethanolamine (DPPE) anddistearoyl phosphatidyl ethanolamine (DSPE). Typically, asurfactant:active substance molar ratio in an aqueous formulation willbe from about 10:1 to about 1:10, more typically from about 5:1 to about1:5, however any effective amount of surfactant may be used in anaqueous formulation to best suit the specific objectives of interest.

When rectally administered in the form of suppositories, theseformulations may be prepared by mixing the compounds according to theinvention with a suitable non-irritating excipient, such as cocoabutter, synthetic glyceride esters or polyethylene glycols, which aresolid at ordinary temperatures, but liquidify and/or dissolve in therectal cavity to release the drug.

Suitable carriers for microcapsules, implants or rods are, for example,copolymers of glycolic acid and lactic acid.

One skilled in this art will recognize that the above description isillustrative rather than exhaustive. Indeed, many additionalformulations techniques and pharmaceutically-acceptable excipients andcarrier solutions are well-known to those skilled in the art, as is thedevelopment of suitable dosing and treatment regimens for using theparticular compositions described herein in a variety of treatmentregimens.

Further, there are several well-known methods of introducing nucleicacids (e.g., antisense and RNAi agents) into animal cells, any of whichmay be used herein. At the simplest, the nucleic acid can be directlyinjected into the target cell/target tissue. Other methods includefusion of the recipient cell with bacterial protoplasts containing thenucleic acid, the use of compositions like calcium chloride, rubidiumchloride, lithium chloride, calcium phosphate, DEAE dextran, cationiclipids or liposomes or methods like receptor-mediated endocytosis,biolistic particle bombardment (“gene gun” method), infection with viralvectors, for example such as taught herein, electroporation, and thelike. Other techniques or methods which are suitable for deliveringnucleic acid molecules to target cells include the continuous deliveryof an NA molecule from poly (lactic-Co-Glycolic Acid) polymericmicrospheres or the direct injection of protected (stabilized) NAmolecule(s) into micropumps delivering the product. Another possibilityis the use of implantable drug-releasing biodegradable micropsheres.Also envisaged is encapsulation of NA in various types of liposomes(immunoliposomes, PEGylated (immuno) liposomes), cationic lipids andpolymers, nanoparticules or dendrimers, poly (lactic-Co-Glycolic Acid)polymeric microspheres, implantable drug-releasing biodegradablemicrospheres, etc; and co-injection of NA with protective agent like thenuclease inhibitor aurintricarboxylic acid. It shall be clear that alsoa combination of different above-mentioned delivery modes or methods maybe used.

A preferred method of intracellular delivery of the antisense agents andRNAi agents disclosed herein may include infection with viral vectors astaught herein. In such method, a recombinant viral vector as taughtherein, is brought in contact with a host cell, such as introduced(e.g., locally or systemically) to a host organism, and incubated atconditions favourable to viral infection and hence, makes use of thenatural ability of a virus to infect a cell. For example, a retrovirusobtains entry to a host cell via the interaction of a retroviral proteinwith a transmembrane protein acting as a receptor on the surface of thehost cell. Another approach of viral vector-mediated delivery ofantisense and RNAi agents as disclosed herein may encompass a physicalcell entry-based technique, such as for example the use of ultrasoundand microbubbles, in combination with viral vector-mediated delivery asdescribed in WO 2006/129080.

Further ways of delivery of nucleic acids such as antisense agents andRNAi agents may employ previously published methods. For example,intracellular delivery of the nucleic acids may be via a compositioncomprising an admixture of the nucleic acid molecule and an effectiveamount of a block copolymer. An example of this method is described inUS 2004/0248833.

Other methods of delivery of nucleic acids to the nucleus are describedin Mann et al. 2001 (Proc Natl Acad Science 98(1): 42-47) and in Gebskiet al. 2003 (Human Molecular Genetics 12(15): 1801-1811).

A method for introducing a nucleic acid molecule into a cell by way ofan expression vector either as naked DNA or complexed to lipid carriers,is described in U.S. Pat. No. 6,806,084.

It may be desirable to deliver a nucleic acid molecule in a colloidaldispersion system. Colloidal dispersion systems include macromoleculecomplexes, nanocapsules, microspheres, beads, and lipid-based systemsincluding oil-in-water emulsions, micelles, mixed micelles, andliposomes or liposome formulations. Liposomes are artificial membranevesicles which are useful as delivery vehicles in vitro and in vivo.These formulations may have net cationic, anionic or neutral chargecharacteristics and are useful characteristics with in vitro, in vivoand ex vivo delivery methods. It has been shown that large unilamellarvesicles (LUV), which range in size from 0.2-4.0 PHI.m can encapsulate asubstantial percentage of an aqueous buffer containing largemacromolecules. RNA, and DNA can be encapsulated within the aqueousinterior and be delivered to cells in a biologically active form (Fraleyet al. 1981 (Trends Biochem ScL 6: 77).

In order for a liposome to be an efficient gene transfer vehicle, thefollowing characteristics should be present: (1) encapsulation of thenucleic acid molecule of interest at high efficiency while notcompromising their biological activity; (2) preferential and substantialbinding to a target cell in comparison to non-target cells; (3) deliveryof the aqueous contents of the vesicle to the target cell cytoplasm athigh efficiency; and (4) accurate and effective expression of geneticinformation (Mannino et al. 1988 (Biotechniques 6: 682).

The composition of the liposome is usually a combination ofphospholipids, particularly high-phase-transition-temperaturephospholipids, usually in combination with steroids, especiallycholesterol. Other phospholipids or other lipids may also be used. Thephysical characteristics of liposomes depend on pH, ionic strength, andthe presence of divalent cations.

Alternatively, the nucleic acid molecule may be combined with otherpharmaceutically acceptable carriers or diluents to produce apharmaceutical composition. Suitable carriers and diluents includeisotonic saline solutions, for example phosphate-buffered saline. Thecomposition may be formulated for parenteral, intramuscular,intravenous, subcutaneous, intraocular, oral or transdermaladministration.

The routes of administration described are intended only as a guidesince a skilled practitioner will be able to determine readily theoptimum route of administration and any dosage for any particular animaland condition. Multiple approaches for introducing functional newgenetic material into cells, both in vitro and in vivo have beenattempted (Friedmann 1989 (Science 244: 1275-1280)). These approachesinclude integration of the gene to be expressed into modifiedretroviruses (Friedmann 1989, supra; Rosenberg 1991 (Cancer Research51(18), suppl.: 5074S-5079S)); integration into non-retrovirus vectors(Rosenfeld et al. 1992 (Cell 68: 143-155); Rosenfeld et al. 1991(Science 252: 431-434)); or delivery of a transgene linked to aheterologous promoter-enhancer element via liposomes (Friedmann 1989,supra; Brigham et al. 1989 (Am J Med Sci 298: 278-281); Nabel et al.1990 (Science 249: 1285-1288); Hazinski et al. 1991 (Am J Resp CellMolec Biol 4: 206-209); and Wang and Huang 1987 (Proc Natl Acad Sci USA,84: 7851-7855)); coupled to ligand-specific, cation-based transportsystems (Wu and Wu 1988 (J Biol Chem 263: 14621-14624)) or the use ofnaked DNA, expression vectors (Nabel et al. 1990, supra); Wolff et al.1990 (Science 247: 1465-1468)). Direct injection of transgenes intotissue produces only localized expression (Rosenfeld 1992, supra;Rosenfeld et al. 1991, supra; Brigham et al. 1989, supra; Nabel 1990,supra; and Hazinski et al. 1991, supra). The Brigham et al. group (Am JMed Sci 298: 278-281 (1989) and Clinical Research 39 (abstract) (1991))have reported in vivo transfection only of lungs of mice followingeither intravenous or intratracheal administration of a DNA liposomecomplex. An example of a review article of human gene therapy proceduresis: Anderson 1992 (Science 256: 808-813).

The pharmaceutical formulations as disclosed herein, which mayconveniently be presented in unit dosage form, may be prepared accordingto conventional techniques well known in the pharmaceutical industry.Such techniques may generally include the step of bringing intoassociation the active ingredients with the pharmaceutical carrier(s) orexcipient(s). In general the formulations are prepared by uniformly andintimately bringing into association the active ingredients with liquidcarriers or finely divided solid carriers or both, and then, ifnecessary, shaping the product.

The present active substances may be used alone or in combination withany other pharmaceutically or biologically active ingredient,particularly which is suitable for the treatment of diseases as taughtherein (“combination therapy”). Combination therapies as contemplatedherein may comprise the administration of at least one active substanceof the present invention and at least one other pharmaceutically orbiologically active ingredient. Said present active substance(s) andsaid pharmaceutically or biologically active ingredient(s) may beadministered in either the same or different pharmaceuticalformulation(s), simultaneously or sequentially in any order.

The dosage or amount of the present active substances used, optionallyin combination with one or more other active compound to beadministered, depends on the individual case and is, as is customary, tobe adapted to the individual circumstances to achieve an optimum effect.Thus, it depends on the nature and the severity of the disorder to betreated, and also on the sex, age, body weight, general health, diet,mode and time of administration, and individual responsiveness of thehuman or animal to be treated, on the route of administration, efficacy,metabolic stability and duration of action of the compounds used, onwhether the therapy is acute or chronic or prophylactic, or on whetherother active compounds are administered in addition to the agent(s) ofthe invention.

Without limitation, depending on the type and severity of the disease, atypical daily dosage might range from about 1 μg/kg to 100 mg/kg of bodyweight or more, depending on the factors mentioned above. For repeatedadministrations over several days or longer, depending on the condition,the treatment is sustained until a desired suppression of diseasesymptoms occurs. A preferred dosage of the active substance of theinvention may be in the range from about 0.05 mg/kg to about 10 mg/kg ofbody weight. Thus, one or more doses of about 0.5 mg/kg, 2.0 mg/kg, 4.0mg/kg or 10 mg/kg (or any combination thereof) may be administered tothe patient. Such doses may be administered intermittently, e.g., everyweek or every two or three weeks.

In an embodiment, a pharmaceutical composition may comprise betweenabout 10 nM and about 1 μM, preferably between about 20 nM and about 600nM, such as, e.g., about 100 nM or about 200 nM, or about 300 nM, orabout 400 nM or about 500 nM of antisense agent or RNAi agent as taughtherein.

Except when noted, “subject” or “patient” are used interchangeably andrefer to animals, preferably warm-blooded animals, more preferablyvertebrates, even more preferably mammals, still more preferablyprimates, and specifically includes human patients and non-human mammalsand primates. Preferred patients are human subjects.

As used herein, a phrase such as “a subject in need of treatment”includes subjects that would benefit from treatment of a givencondition, particularly of facioscapulohumeral muscular dystrophy (FSHD)or a tumour, such as preferably a sarcoma, such as more preferably asarcoma selected from Ewing's family tumours, paediatricundifferentiated soft tissue sarcomas and rhabdomyosarcomas. Suchsubjects may include, without limitation, those that have been diagnosedwith said condition, those prone to contract or develop said conditionand/or those in whom said condition is to be prevented.

The terms “treat” or “treatment” encompass both the therapeutictreatment of an already developed disease or condition, such as thetherapy of an already developed FSHD or tumour, such as preferably asarcoma, such as more preferably a sarcoma selected from Ewing's familytumours, paediatric undifferentiated soft tissue sarcomas andrhabdomyosarcomas, as well as prophylactic or preventative measures,wherein the aim is to prevent or lessen the chances of incidence of anundesired affliction, such as to prevent the chances of contraction andprogression of FSHD or a tumour, such as preferably a sarcoma, such asmore preferably a sarcoma selected from Ewing's family tumours,paediatric undifferentiated soft tissue sarcomas and rhabdomyosarcomas.Beneficial or desired clinical results may include, without limitation,alleviation of one or more symptoms or one or more biological markers,diminishment of extent of disease, stabilised (i.e., not worsening)state of disease, delay or slowing of disease progression, ameliorationor palliation of the disease state, and the like. “Treatment” can alsomean prolonging survival as compared to expected survival if notreceiving treatment.

The term “prophylactically effective amount” refers to an amount of anactive compound or pharmaceutical agent that inhibits or delays in asubject the onset of a disorder as being sought by a researcher,veterinarian, medical doctor or other clinician. The term“therapeutically effective amount” as used herein, refers to an amountof active compound or pharmaceutical agent that elicits the biologicalor medicinal response in a subject that is being sought by a researcher,veterinarian, medical doctor or other clinician, which may include interalia alleviation of the symptoms of the disease or condition beingtreated. Methods are known in the art for determining therapeuticallyand prophylactically effective doses for the present compounds.

Reference to “diseases or conditions comprising increased levels and/orincreased activity of double homeobox 4 and/or double homeobox 4c”generally covers diseases and conditions in which the level and/oractivity of DUX4 and/or DUX4c is increased by any (measurable) extentcompared to a reference non-disease state, such as without limitation isincreased by at least about 10%, e.g., by at least about 20%, preferablyby at least about 30%, e.g., by at least about 40%, more preferably byat least about 50%, e.g., by at least about 75%, even more preferably byat least about 100%, e.g., by at least about 150%, 200%, 250%, 300%,400% or by at least about 500%, compared to a reference non-diseasestate. The term also covers situations in which a reference non-diseasestate comprises no demonstrable level and/or activity of DUX4 and/orDUX4c whereas a disease state comprises some demonstrable level and/oractivity of DUX4 and/or DUX4c. The level and/or activity of DUX4 and/orDUX4c may be increased in any cells, tissues and/or organs of a patient,preferably in cells, tissues and/or organs relevant to or affected in adisease or condition. For example, the level and/or activity of DUX4and/or DUX4c may be increased in muscle cells and muscle tissues, suchas, e.g., in myoblasts and/or in myocytes, in smooth muscles and/or instriated muscles such as in skeletal and or cardiac muscles, etc.

The level of DUX4 and/or DUX4c may be measured at any one or morestages, such as at the stage of pre-mRNA or mRNA (e.g., by qualitativeor quantitative RT-PCR) and/or protein (e.g., immunoassay methods). Theactivity of DUX4 and/or DUX4c protein may be measured by any suitablebiochemical or cellular assays, e.g., measuring its trans-activationpotential on known targets.

Facioscapulohumeral muscular dystrophy (FSHD, FSHMD or FSH) also knownas Landouzy-Dejerine muscular dystrophy encompasses all diseases andcondition known under these designations in the art. More particularly,FSHD as intended herein is an autosomal dominant muscle disordergenetically linked to contractions of the D4Z4 repeat array on the 4q35subtelomeric region, more particularly where FSHD patients have between1 and 10 D4Z4 copies, such as e.g., 2, 3, 4, 5, 6, 7, 8 or 9 copies.Also particularly, FSHD may be linked to the 4qA allele, even moreparticularly to the permissive alleles 4A161, 4A161L, 4A159 or 4A168.

Moreover, although a small group of patients with a typical FSHDphenotype presents more than 10 copies of the D4Z4 element, thesepatients show sub-normal DNA methylation level at the repeat, similar tothat found in contracted D4Z4 arrays. Consequently, FSHD can begenerally concluded when DNA hypomethylation is observed at the D4Z4repeat, irrespective of the number of D4Z4 units.

Diseases or conditions the treatment of which can benefit from reducingthe expression of double homeobox 4 and/or double homeobox 4c alsospecifically encompass those which comprise expression of DUX4 and/orDUX4c fragments or variants, more particularly expression of fusionproteins between DUX4 or DUX4c (preferably DUX4) and other, unrelatedproteins, more preferably, such fusion proteins comprising theC-terminal fragment of DUX4 or DUX4c (preferably DUX4), even morepreferably such fusion proteins with CIC, a human homolog of Drosophilacapicua, or with EWSR1. Said fusion proteins are commonly expressed as aresult of chromosomal rearrangements and favour cell proliferation andhence, may cause tumours, such as in particular Ewing's family tumours(EFTs) (Kawamura-Saito et al. 2006, supra) and paediatricundifferentiated soft tissue sarcomas (Yoshimoto et al. 2009, supra) andrhabdomyosarcomas (Sirvent et al. 2009, supra), respectively. Since saidfusion mRNAs include the sequence elements of the DUX4 or DUX4c genes(preferably the DUX4 gene) that are targeted by the antisense agentsand/or RNAi agents as described herein, these tools may reduce theexpression of said fusion proteins similarly as they reduce theexpression of the full length DUX4 or DUX4c protein. Hence, diseases andconditions intended herein also include tumours, more particularlysarcomas, even more particularly the aforementioned tumour types. Asused herein, the term “tumour” refers to an abnormal mass of tissue thatresults from excessive cell division. A tumour comprises “tumour cells”which are neoplastic cells with abnormal growth properties and may alsocomprise “tumour-associated non-tumour cells”, e.g., vascular cellswhich form blood vessels to supply the tumour. A tumour may be benign ormalignant. The term “sarcoma” encompasses tumour types involvingconnective tissue cells, such as for example but without limitationbone, cartilage, fat cells, muscles and blood vessels.

It is apparent that there have been provided in accordance with theinvention products, methods and uses that provide for substantialadvantages as set forth above. While the invention has been described inconjunction with specific embodiments thereof, it is evident that manyalternatives, modifications, and variations will be apparent to thoseskilled in the art in light of the foregoing description. Accordingly,it is intended to embrace all such alternatives, modifications, andvariations as follows in the spirit and broad scope of the appendedclaims

The above aspects and embodiments are further supported by the followingnon-limiting examples.

EXAMPLES Example 1 Antisense Oligonucleotides Directed Against SequenceElements Involved in Splicing of DUX4 Pre-mRNA are Highly Effective inDown-Regulating Double Homeobox 4 Expression

Antisense oligomers (AO) were designed based on the sequence of the DUX4gene 3′ UTR (FIG. 1). The 7 AO include one (JSR 1521 pLAM2A) directedagainst positions −7+18 of DUX4 intron 1-exon 2 boundary (incl. intron 1splice acceptor site), and six AO directed against DUX4 intron 2-exon 3boundary (incl. intron 2 splice acceptor site), denoted JSR 1522pLam3A(−7+18), JSR1523 pLAM3A (−12+13), JSR1524 pLAM3A (−2+23), JSR1696pLAM3A (−7+18), JSR1719 pLAM3A (−12+18) and JSR1720 pLAM3A (−17+13). AnAO targeting dystrophin was used as negative control.

Anti-DUX4 AO: JSR 1521 pLAM2A (−7 + 18): CUCUCACCGGGCCUAGACCUAGAAG(SEQ ID NO: 16) JSR 1522 pLam3A (−7 + 18): UGCGCACUGCGCGCAGGUCUAGCCA(SEQ ID NO: 17) JSR1523 pLAM3A (−12 + 13): ACUGCGCGCAGGUCUAGCCAGGAAG(SEQ ID NO: 18) JSR1524 pLAM3A (−2 + 23): CGGGGUGCGCACUGCGCGCAGGUCU(SEQ ID NO: 19) JSR1696 pLAM3A (−7 + 18): UGCGCACUGCGCGCAGGUCUAGCCA(SEQ ID NO: 17) JSR1719 pLAM3A(−12 + 18): UGCGCACUGCGCGCAGGUCUAGCCAGGAAG(SEQ ID NO: 20) JSR1720 pLAM3A (−17 + 13):ACUGCGCGCAGGUCUAGCCAGGAAGCGGGC (SEQ ID NO: 21)AO targeting dystrophin (negative controls) JSR 1662 mGMCSF3A (−05 +20): UCCCACAGAAGCUAACAUGUGUGCAGAC

All AO used in this example had 2′-O-methyl-phosphorothioate backbone.AO having phosphorodiamidate morpholino backbone are used with at leastcomparable or superior results. AO conjugated to a cell penetratingpeptide (CPP) are used with at least comparable or superior results.

Testing C2C12 Mouse Myoblasts Transiently Expressing Dux4

The efficacy of antisense oligonucleotides (AO) against the DUX4pre-mRNA was evaluated in transient expression in C2C12 mouse myoblastsgrown in vitro. These cells were transfected with the pCIneo-DUX4expression vector that contains the DUX4 coding region of the last D4Z4element and the flanking pLAM region under the strong CMV promoter.

10⁵ C2C12 mouse myoblasts were seeded per well of 6-well dishes andgrown at 37° C. and 5% CO₂ in DMEM, 10% foetal bovine serum gold (PAA),1% antibiotics (penicillin, streptomycin, fungizon). They weretransfected 24 hours later with 500 ng per well of expression vectorpCIneo-DUX4 alone or combined with the indicated AO. The negativecontrol is AO 1662 that targets the dystrophin mRNA. The transfectionreagent was Lipofectamine™ 2000 (Invitrogen) used at a ratio of 1 μgAO/1 μl reagent, and 600 nM AO concentration. The cells were lysed 24hours after transfection, and total protein extracts were prepared inNuPAGE® LDS sample buffer (Invitrogen). 15 μg of protein extracts wereseparated by electrophoresis (SDS-PAGE 12%), and transferred to anitrocellulose membrane. DUX4 (52 kDa) was detected on this Western blotwith the 9A12 monoclonal antibody followed by anti-mouse IgG antibodiescoupled to peroxidase (HRP), and revealed with Lumi-Light kit (Roche)detected on a film. After striping these antibodies, the same membranewas incubated with an anti-actin antibody to provide a loading control.The mouse monoclonal antibody (MAb 9A12) was raised as described inDixit et al. 2007 (supra) directed against the carboxyl terminal part ofDUX4. Whereas this antibody cross reacts with DUX4c, the two proteinscan be readily distinguished in Western blot based on their differentapparent molecular weights, i.e., 52 kDa for DUX4 and 47 kDa for DUX4c.

The results are shown in FIG. 9. No DUX4 protein (arrow) could bedetected by Western blot using the 9A12 monoclonal antibody followingthe addition of different AO directed against the DUX4 pre-mRNA. Incontrast the DUX4 protein was clearly expressed with the AO directedagainst the dystrophin pre-mRNA or in the absence of AO.

Testing C2C12 Mouse Myoblasts Transiently Expressing Dux4 or Dux4c

Another experiment demonstrates, using the above-explained transientexpression approach, that AO 1524 can achieve specific downregulation ofDUX4 expression without affecting DUX4c protein expression (FIG. 10).C2C12 cells were transfected with either the expression vectorpCIneo-DUX4 or pCIneo-DUX4c, alone or with different concentrations ofAO 1524 targeting the DUX4 mRNA, or the negative control AO 1662(concentration of 600 nM). DUX4 and DUX4c proteins were detected on aWestern blot of cell protein extracts as described above. In thisexperiment 100 nM AO (boxed in FIG. 10) substantially suppressed DUX4protein detection on the Western blot but did not affect DUX4c levels,thereby demonstrating specificity of the targeting by this AO.

Testing C2C12 Mouse Myoblasts Transiently Expressing Dux4 and Dux4c

Similar results have been obtained in a co-transfection experiment inC2C12 cells using both DUX4 and DUX4c pCIneo expression vectors, so thatboth mRNAs were present simultaneously in the same cells. C2C12 cellswere co-transfected with both pCIneo-DUX4 and pCIneo-DUX4c expressionvectors, with different concentrations of AO 1524 targeting the DUX4mRNA, or the negative control AO 1662 (600 nM). The DUX4 and DUX4cproteins were detected on a Western blot of cell protein extracts asdescribed above. In this experiment 150 nM AO (FIG. 11) substantiallysuppressed DUX4 protein detection on the Western blot but did not affectDUX4c levels, thereby further corroborating specificity of the targetingby this AO.

In analogous co-transfection studies using the other AO, comparablespecificity for DUX4 was also demonstrated for AO 1522 and 1523 (using150 nM AO, see FIG. 12) and AO 1521 (using 50 nM AO, not shown).Moreover, lower concentrations in this experiment achieve comparablespecificity for A01719 and 1720.

Testing FSHD Primary Myoblasts Endogenously Expressing DUX4

To test the efficacy of AOs 1521 pLAM2A(−7+18) and 1523 pLAM3A(−12+13)on endogenous DUX4 expression, primary FSHD myoblasts were transfectedwith 50 nM 1521 pLAM2A(−7+18) or with 150 nM 1523 pLAM3A(−12+13) or with600 nM of the negative control AO (nc-AO; JSR 1662 mGMCSF3A (−5+20)).Differentiation was induced 4 hours after transfection and three dayslater myotubes were lysed for total RNA extraction. Reversetranscription (RT) was performed on 500 ng of DNase-treated myotubetotal RNA using the FirstChoice® RLM-RACE kit (Ambion). 5 μl of theresulting cDNA were amplified by nested PCR with primers previouslyshown to be specific of the DUX4 mRNA 3′UTR (Dixit et al. 2007. supra).GAPDH mRNA amplification was used as an internal control. The RT-PCRproducts were analysed by electrophoresis on a 1% agarose gel. Adensitometry of the bands was performed for quantification. Data werenormalized to GAPDH mRNA levels.

FIG. 29 shows that the expected 550 bp DNA fragment was detected in FSHDmyotubes treated with nc-AO and at a 30% and 50% reduced intensity incells treated with AOs 1521 pLAM2A(−7+18) (FIG. 29 a) or 1523pLAM3A(−12+13) (FIG. 29 b), respectively. This amplicon was alsoobserved in the positive control, i.e. C2C12 cells transfected withpGEM42, but not in the negative controls, i.e. either C2C12 cellstransfected with the empty pGEM vector, or primary myoblasts from ahealthy donor, or upon omission of reverse transcriptase. The RT-PCRproducts were cloned and sequenced to confirm DUX4 mRNA amplification(data not shown).

Example 2 siRNA (Small Interfering RNA) Directed Against 3′UTR Region ofDUX4 or DUX4c mRNA Achieve Specific Silencing of DUX4 or DUX4cExpression

Anti-DUX4 siRNA agents were developedbased on and comprising the following DUX4 mRNA sequences:(SEQ ID NO: 47) siRNA-DUX41: acaccuggcuggcuacgga (SEQ ID NO: 48)siRNA-DUX42: ggucuaggcccggugagag (SEQ ID NO: 49) siRNA-DUX43:ccuggauuagaguuacauc. Anti-DUX4c siRNA agents were developedbased on the following DUX4c mRNA sequences: (SEQ ID NO: 56)siRNA-DUX4c1: ccagaguuucagcaaaagg; (SEQ ID NO: 57) siRNA-DUX4c2:ggagggcugucauucuuuc; (SEQ ID NO: 58) siRNA-DUX4c3: gcguucuucagucgaguug.

Cells were transfected using the “Silencer siRNA Starter Kit” (Ambion)containing the transfection agent SiPORT™ NeoFX™ (Ambion). TE671 cells(cells derived from a human alveolar rhabdomyosarcoma) were used fortransfections, using the “reverse” method recommended by the supplier,in which the transfection reagent is introduced into the culture dishbefore seeding the cells. This method was three times superior than thetraditional method in our hands. Transfection conditions were optimisedusing control anti-GAPDH siRNA supplied with the above kit. Theoptimised conditions included 2 μl SiPORT™ NeoFX™ reagent, 10 nM siRNA,and 5×10⁴ cells/ml cell density.

Testing a TE671 Cell Line with an Inducible DUX4c Transgene

The efficiency of siRNA directed against the DUX4c mRNA was tested usingstable TE671-DUX4c lines established previously. These cells haveincorporated the pAC1M2-DUX4c expression vector in which DUX4ctranscription is inducible by doxycycline (DOX).

The cells were first transfected using the above conditions, which leadto only a weak DUX4c inhibition. Therefore the siRNA concentration wasincreased to 20 nM that was not toxic to the cells.

The cells were seeded at a density of 1×10⁵ cells/well of a 6 wellculture dish and transfected with siRNA-DUX4c1 20 nm (“si”) by thereverse transfection method (Ambion). 4 hours after transfection, theexpression of DUX4c was induced (“I”) by adding 1 mg/ml of doxycyclinein the culture medium. The 3rd or 5th day after induction, the cellswere lysed and 20 μg of protein extracts were analyzed by SDS-PAGEelectrophoresis (10%), and transferred to a nitrocellulose membrane. Themembrane was incubated with the anti-DUX4c rabbit serum directed againsta peptide in the carboxyterminal domain followed by a secondary antibodycoupled to peroxidase and revealed with the kit LiteABlot® (Euroclone).DUX4c protein expression (nuclear staining) was also analysed byimmunohistochemistry in TE-DUX4c cells transfected with siRNA-DUX4c1.The cells were transfected and DUX4c expression was induced as explainedabove. The 3rd or 5th day after induction, cells were fixed in PAF andincubated with anti-DUX4c rabbit serum and secondary antibodies coupledto a red dye (Alexa Fluor®). Pictures were taken under a fluorescencemicroscope after selecting a field where many cells were visible inwhite light.

After three days, a significant decrease of the DUX4c protein amountcould be observed in extracts from cells treated with siRNA 1 comparedto untreated cells as well by Western blot (FIG. 13A) as byimmunofluorescence (not shown). After five days, DUX4c expressionincreased again in the transfected cells (FIG. 13A), which could beexplained by a possible degradation or dilution of the siRNA with time.Similar data has been obtained using siRNA-DUX4c 2 (“si2”) or 3 (“si3”)compared to a negative control siRNA (“SiCN”) at 3rd day after inductionof DUX4c expression (FIG. 13B).

Testing a TE671 Cell Line Transiently Expressing DUX4c

To confirm the results obtained on stable TE671-DUX4c line, we repeatedthe experiment on TE671 cells. We transfected cells with the siRNA andfour hours later with the pCIneo-DUX4c expression vector which containsthe strong cytomegalovirus promoter/enhancer.

The cells were transfected with siRNA-DUX4c 20 nM (“si1”, “si2” and“si3”) or negative control siRNA (“SiCN”) using reverse transfection(Ambion) and 4 hours later with the pCIneo-DUX4c vector (DUX4c). Theprotein extracts were prepared and cells were fixed the third day aftertransfection of the pCIneo-DUX4c vector. The methodologies for theWestern blot and immunofluorescence were as set out above.

An inhibition of DUX4c expression similar to the previous experiment wasobserved by Western blot (FIG. 14) and immunofluorescence (not shown).We selected siRNA 1 as the most effective.

Testing a TE671 Cell Line Transiently Expressing DUX4

Using similar methodology as in the previous section (except that thegel is a SDS-PAGE 12%, the primary antibody is the 9A12 monoclonalantibody), we first transfected TE671 cells using the reversetransfection method with each of the three siRNA against DUX4. Fourhours later we transfected these cells with the pCIneo-DUX4 expressionvector. Three days after the second transfection, the DUX4 expressionhad completely disappeared in cells treated with siRNA as well onWestern blot (FIG. 15) as in immunofluorescence (not shown). We selectedthe siRNA 3 for further studies as it targets a region particularlyspecific of DUX4.

Specificity of the Selected siRNAs

TE671 cells were transfected with siRNA-DUX4c (“siDUX4c”) or siRNA-DUX4(“siDUX4”) (20 nM) using reverse transfection and 4 hours later with thepCIneo-DUX4 (“DUX4”) or pCIneo-DUX4c (“DUX4c”) expression vector. Theprotein extracts were prepared on the third day after pCIneo vectorstransfection and revealed by Western blot with the 9A12 monoclonalantibody and secondary antibodies coupled to HRP. The antibodies werethen stripped, and the same membrane developed with an anti-actin serum(internal control).

The siRNA specificity was confirmed by the disappearance, in westernblot, of bands corresponding to the molecular weight of DUX4 or DUX4cfollowing the addition of their respective siRNA and not with the siRNAof their homologue (FIG. 16).

Construction of shRNA (Small Hairpin RNA) Vectors

To test the effect of siRNA on FSHD myotubes, we used lentiviral vectorsto produce shRNAs that are processed in the cell to yield identicalsiRNAs to those that we selected (FIG. 17). It has been previouslydemonstrated that myoblasts and myotubes could be efficiently transducedby such vectors. For this, synthetic DNA corresponding to the sequencesof selected siRNA (sense sequence+loop (CTCGAG)+antisense sequence) wereinserted into an expression vector containing the promoter of thehistone H1 gene. Hence, the transcription unit contains the followingelement: H1 promoter ---CCGG(sense strand)loop(anti-sensestrand)TTTTT---. Transcription produces shRNA which is processed tosiRNA by Dicer (see FIG. 18). The H1-shRNA gene was sub-cloned in apLVTH vector containing all the necessary elements for encapsidation.

Prior to encapsidation, we have checked the efficiency of pLVTH-shRNAvectors by Western blot on TE671 cells co-transfected with these vectorsand with pCIneo-DUX4 or DUX4c expression vector.

FIG. 19 shows Western blot analysis of DUX4 protein expression onextracts of TE671 cells transfected with the pCIneo-DUX4 expressionvector alone (“TE+DUX4”) or with shRNA-DUX4 (“TE DUX4+shDUX4”) orshRNA-DUX4c (“TE DUX4+shDUX4c”) (Fugene 6, Roche Molecular Biochemical).48 hours after transfection, proteins were extracted and 20 μg of theseextracts were analyzed by SDS-PAGE electrophoresis (12%), thentransferred to a nitrocellulose membrane. The membrane was incubatedwith 9A12 MAb followed by a secondary antibody coupled to peroxidase andrevealed with the LiteABlot® kit (Euroclone). The antibodies were thenstripped, and the same membrane revealed with an anti-actin serum(internal control). Immunofluorescence analysis of DUX4c proteinexpression (nuclear staining) in TE671 cells transfected with thepCIneo-DUX4c vector alone or with shRNA-DUX4 or shRNA-DUX4c wasperformed (Fugene 6). 48 hours after transfection, cells were fixed in4% PAF and incubated with anti-DUX4c and a secondary antibody coupled toa red dye (Alexa Fluor®) (not shown).

A decrease in intensity of the band corresponding to 52 kDa DUX4 (FIG.19) and of the DUX4c signal in immunofluorescence (not shown) wasconfirmed following the addition of their respective shRNA.

Once their efficiency was proven, we encapsidated the pLVTH-shRNAvectors. We then co-transduced immortal control myoblasts withrecombinant lentivirus expressing either DUX4 or DUX4c and recombinantlentivirus expressing their respective shRNA. 72 hours aftertransduction, we detected by immunofluorescence the DUX4 and DUX4cproteins using monoclonal antibody 9A12. The presence of shRNA in thecells is confirmed by the expression of GFP encoded by the shRNA vector.

After 72 hours, a decreased expression of both proteins following theaddition of their respective shRNA was visible by immunofluorescence(not shown).

Testing FSHD Primary Myoblasts Endogenously Expressing DUX4

Human FSHD primary myoblasts, which are difficult to transfect, weretransfected following the reverse transfection method as described aboveusing the “Silencer siRNA Starter Kit” (Ambion). Optimal transfectionconditions, defining an effective transfection reagent with lowcytotoxicity for human primary myoblasts, were set up using controlanti-GAPDH siRNA supplied with the above kit. 72 hours aftertransfection, cells were harvested and 10 μg of protein extracts wereseparated by SDS-PAGE (12%) and transferred to a nitrocellulosemembrane. The protein transfer was confirmed by staining the membranewith Ponceau red. After rinsing the membrane, it was incubated withanti-GAPDH monoclonal antibody, followed by a secondary antibody coupledto horseradish peroxidase and revealed with the Lumilight substrate(Roche) followed by detection on a photographic film. Optimaltransfection conditions included 4 μl SiPORT™ NeoFX™ reagent, 20 nMsiRNA, and a cell density of 10⁵ cells in a 35 mm culture dish (FIG.22).

To test the efficiency of siRNA directed against the DUX4 mRNA, wetransfected FSHD primary myoblasts with the siRNA using the transfectionconditions specified above.

The cells were seeded at a density of 10⁵ cells in a 35 mm culture dishand transfected with control siRNA or DUX4-siRNA3 following the reversetransfection method using 4 μl SiPORT™ NeoFX™ reagent. 3 differentDUX4-siRNA3 concentrations were tested (10 nM, 20 nM and 30 nM) todetermine the best concentration to use to reduce the endogenous DUX4expression. Since the DUX4 protein is only detectable in myotubes, 4hours after transfection, myoblasts differentiation was induced byreplacing the culture medium by a medium without serum. Cells wereharvested 72 h after differentiation and nuclear protein extracts wererealised. 20 μg of these nuclear protein extracts and 5 μg of nuclearprotein extract of TE671 cells that were transfected with thepCIneo-DUX4 expression vector (TE-DUX4), which was used as a positivecontrol, were separated by SDS-PAGE (12%) and transferred onto anitrocellulose membrane. Protein transfer was confirmed by staining themembrane with Ponceau red (not shown). After rinsing the membrane, itwas incubated with the 9A12 monoclonal antibody followed by a secondaryantibody coupled to horseradish peroxidase and revealed with the FemtoSuper Signal kit (Pierce) followed by detection on a photographic film.The antibodies were then stripped and the same membrane wasimmunostained with a TBP monoclonal antibody as a nuclear loadingcontrol.

After three days, a significant decrease of the DUX4 protein amount, asindicated by the red arrow, could be observed in protein extracts fromcells treated with DUX4-siRNA compared to cells treated with the controlsiRNA by Western blot (FIG. 23).

The efficiency of the siRNA targeting the DUX4 mRNA was confirmed byRT-PCR as a decrease of endogenous DUX4 mRNA amount in FSHD primarymyotubes. FSHD primary myoblasts were transfected with 10 nM DUX4-siRNA3 or control siRNA (30 nM) using the transfection conditions specifiedabove. 4 hours after transfection, myoblast differentiation was inducedas specified above. Following differentiation for 3 days, total RNA wasextracted from the myotubes. Reverse transcription (RT) was performed on500 ng of DNase-treated myotube total RNA using the FirstChoice®RLM-RACEkit (Ambion). 5 μl of the resulting cDNA were amplified by nested PCRwith primers previously shown to be specific of the DUX4 mRNA 3′UTR(Dixit et al. 2007. supra). GAPDH mRNA amplification was used as aninternal control. The RT-PCR products were analysed by electrophoresison a 1% agarose gel. A densitometry of the bands was performed forquantification. Data were normalized to GAPDH mRNA levels.

As shown in FIG. 30, the expected 550 bp DNA fragment was detected inFSHD myotubes transfected with the control siRNA (nc-siRNA) and at a 80%reduced intensity in cells treated with the DUX4-siRNA 3. This ampliconwas also observed in the positive control i.e. C2C12 cells transfectedwith the pGEM42 vector containing two D4Z4 units (Gabriëls et al. 1999.supra) but not in primary myoblasts from a healthy donor (Cont), or uponomission of reverse transcriptase. The RT-PCR products were cloned andsequenced to confirm DUX4 mRNA amplification (data not shown).

Example 3 Further Antisense Oligonucleotides Directed Against DUX4Pre-mRNA

Two further antisense oligomers (AO) directed against the DUX4 pre-mRNAwere designed based on the DUX4 gene sequence. One of these AOs, JSR2245 pLAM polyA (−13+6), is capable of binding to a sequence elementrequired for polyadenylation of the DUX4 mRNA. The other AO, JSR 2250pLAM1D (+7−18 around exon-1 intron-1 boundary), is capable of binding toa sequence element located in the 3′ untranslated sequence of the DUX4mRNA between the stop codon and the first intron (see FIG. 31). WhereasJSR 2250 pLAM1D binds to an exon-intron boundary, it does not in aninitial experiment appear to interfere with splicing of DUX4.

JSR 2245 pLAM polyA (−13 + 6): (SEQ ID NO: 65) GGGCAUUUUAAUAUAUCUCUGAACUJSR 2250 pLAM1D (+7 − 18): (SEQ ID NO: 64) ACCCGACCCCGUCCCAACCCCGCGU

Both AOs had 2′-O-methyl-phosphorothioate backbone.

The efficacy of both AOs, JSR 2245 and JSR 2250, was evaluated intransient expression in C2C12 mouse myoblasts grown in vitro that wereco-transfected with both DUX4 and DUX4c pCIneo expression vectors, sothat both mRNAs were present simultaneously in the same cells.

10⁵ C2C12 mouse myoblasts were seeded per well of 6-well dishes andgrown at 37° C. and 5% CO₂ in DMEM, 10% foetal bovine serum gold (PAA),1% antibiotics (penicillin, streptomycin, fungizon). They wereco-transfected 24 hours later with 500 ng per well of the expressionvectors pCIneo-DUX4 and pCIneo-DUX4c combined with the indicated AO. Asthe 150 nM concentration seemed to be most effective in previousexperiments (see Example 1), we tested the effect of the AOs 2245 and2250 targeting the DUX4 mRNA using this concentration. The negativecontrol was AO 1662 that targets the dystrophin mRNA and was used at aconcentration of 600 nM. The transfection reagent was Lipofectamine™2000 (Invitrogen) used at a ratio of 1 μg AO/1 μl reagent. The cellswere lysed 24 hours after transfection, and total protein extracts wereprepared in NuPAGE® LDS sample buffer (Invitrogen). 15 μg of proteinextracts were separated by electrophoresis (SDS-PAGE 12%), andtransferred to a nitrocellulose membrane. DUX4 (52 kDa) was detected onthis Western blot with the 9A12 monoclonal antibody followed byanti-mouse IgG antibodies coupled to peroxidase (HRP), and revealed withLumi-Light kit (Roche) detected on a film After striping theseantibodies, the same membrane was incubated with an anti-actin antibodyto provide a loading control.

The results are shown in FIG. 32. In the conditions as specified above,AO 2250 could strongly reduce DUX4 levels as compared to the negativecontrol AO 1662 while DUX4c was still expressed. In contrast AO 2245suppressed both DUX4 and DUX4c proteins at this concentration,suggesting that yet lower amounts may need to be used in case specifictargeting of DUX4 production is intended (FIG. 32).

In a similar experiment, AO 2245 was used at a concentration of 10, 25,50, 100 or 150 nM. The optimal concentration for specifically inhibitingDUX4 protein expression was found to be 50 nM (FIG. 33).

What is claimed is:
 1. A method for treating a disease or condition the treatment of which can benefit from reducing the expression of double homeobox 4 and/or double homeobox 4c in a subject, comprising administering to said subject a therapeutically or prophylactically effective amount of one or more agents selected from the group consisting of: an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes; a nucleic acid encoding an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes; a recombinant nucleic acid construct or vector comprising a nucleic acid encoding an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes; a host cell or a progeny thereof comprising an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, a nucleic acid encoding an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, or a recombinant nucleic acid construct or vector comprising a nucleic acid encoding an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes; a host organism or a progeny thereof comprising an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, a nucleic acid encoding an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, a recombinant nucleic acid construct or vector comprising a nucleic acid encoding an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, or a host cell or a progeny thereof comprising an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, a nucleic acid encoding an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, or a recombinant nucleic acid construct or vector comprising a nucleic acid encoding an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes; or a composition or formulation comprising an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, a nucleic acid encoding an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, a recombinant nucleic acid construct or vector comprising a nucleic acid encoding an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, a host cell or a progeny thereof comprising an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, a nucleic acid encoding an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, or a recombinant nucleic acid construct or vector comprising a nucleic acid encoding an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, or a host organism or a progeny thereof comprising an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, a nucleic acid encoding an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, a recombinant nucleic acid construct or vector comprising a nucleic acid encoding an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, or a host cell or a progeny thereof comprising an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, a nucleic acid encoding an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes, or a recombinant nucleic acid construct or vector comprising a nucleic acid encoding an antisense agent capable of binding to the double homeobox 4 (DUX4) and/or double homeobox 4c (DUX4c) genes.
 2. The method according to claim 1, wherein the disease or condition is facioscapulohumeral muscular dystrophy (FSHD).
 3. The method according to claim 1, wherein the disease or condition is a sarcoma comprising expression of a fusion protein between DUX4 or DUX4c and another, unrelated protein.
 4. The method according to claim 1, wherein the antisense agent is capable of binding to the DUX4 gene but not to the DUX4c gene.
 5. The method according to claim 1, wherein the antisense agent is capable of binding to the DUX4c gene but not to the DUX4 gene.
 6. The method according to claim 1, wherein the antisense agent is an antisense molecule.
 7. The method according to claim 6, wherein the antisense molecule is an antisense nucleic acid molecule, an antisense nucleic acid analogue molecule, an antisense oligonucleotide or an antisense oligonucleotide analogue.
 8. The method according to claim 1, wherein the antisense agent is between about 10 and about 100, between about 12 and about 80, between about 15 and about 50, between about 20 and about 40, or between about 20 and about 30 nucleotides or nucleotide analogues in length.
 9. The method according to claim 1, wherein the antisense agent is an antisense oligonucleotide analogue comprising a 2′-O-methylated phosphorothioate backbone or a phosphorodiamidate morpholino backbone.
 10. The method according to claim 1, wherein the antisense agent is conjugated to a cell penetrating peptide (CPP).
 11. The method according to claim 1, wherein the antisense agent is capable of binding to a sequence element required for splicing of the DUX4 or DUX4c genes.
 12. The method according to claim 11, wherein the antisense agent is capable of binding to a sequence element required for splicing of the DUX4 gene, but not required for splicing of the DUX4c gene.
 13. The method according to claim 11, wherein the antisense agent is capable of binding to a sequence element required for splicing of the DUX4c gene, but not required for splicing of the DUX4 gene.
 14. The method according to claim 11, wherein the sequence element required for splicing of the DUX4 or DUX4c genes is selected from the group consisting of splice donor sites, splice acceptor sites, pyrimidine-rich or polypyrimidine tracts upstream of splice acceptor sites, exon-intron boundaries, intron-exon boundaries, branch sites and exonic splicing enhancer elements of the DUX4 or DUX4c genes.
 15. The method according to claim 14, wherein the sequence element required for splicing of the DUX4 or DUX4c genes is selected from the group consisting of splice donor sites, splice acceptor sites, exon-intron boundaries and intron-exon boundaries of the DUX4 or DUX4c genes.
 16. The method according to claim 1, wherein the antisense agent is configured to bind to at least about 10 bases, at least about 15 bases, at least about 20 bases, at least about 25 bases, at least about 30 bases, between about 10 and about 40 bases, or between about 20 and about 30 bases of any one of the following DUX4 sequences (SEQ ID NO: 2, 4, 6, 8) or of variants thereof having at least about 80%, at least about 90% or at least about 95% sequence identity to the respective sequences: (SEQ ID NO: 2) ggctctgctggaggagctttaggacgcggggttgggacggggtcgggtggttcggggcag; (SEQ ID NO: 4) gctgaccggcctgggattcctgccttctaggtctaggcccggtgagagactccacaccgc; (SEQ ID NO: 6) ggcatcccggggatcccagagccggcccaggtacctgcgcacgcgcgggtttgcgggcag; or (SEQ ID NO: 8) tctgtctgtctttgcccgcttcctggctagacctgcgcgcagtgcgcaccccggctgacg.


17. The method according to claim 1, wherein the antisense agent comprises a sequence complementary to any one of the following DUX4 sequences (SEQ ID NO: 10 to 15, 66) or to variants thereof having at least about 80%, at least about 90% or at least about 95% sequence identity to the respective sequences, or to fragments thereof comprising at least about 10 bases, at least about 12 bases, at least about 15 bases, at least about 20 bases, or at least about 25 bases of the respective sequences or variants of: (SEQ ID NO: 10) cttctaggtctaggcccggtgagag; (SEQ ID NO: 11) tggctagacctgcgcgcagtgcgca; (SEQ ID NO: 12) cttcctggctagacctgcgcgcagt; (SEQ ID NO: 13) agacctgcgcgcagtgcgcaccccg; (SEQ ID NO: 14) cttcctggctagacctgcgcgcagtgcgca; (SEQ ID NO: 15) gcccgcttcctggctagacctgcgcgcagt; or (SEQ ID NO: 66) acgcggggttgggacggggtcgggt.


18. The method according to claim 1, wherein the antisense agent is an anti-DUX4 antisense agent comprising any one of sequences (SEQ ID NO: 16 to 21, 64) or variants thereof having at least about 80%, at least about 90% or at least about 95% sequence identity to the respective sequences, or fragments thereof comprising at least about 10 bases, at least about 12 bases, at least about 15 bases, at least about 20 bases, or at least about 25 bases, of the respective sequences or variants: (SEQ ID NO: 16) CUCUCACCGGGCCUAGACCUAGAAG; (SEQ ID NO: 17) UGCGCACUGCGCGCAGGUCUAGCCA; (SEQ ID NO: 18) ACUGCGCGCAGGUCUAGCCAGGAAG; (SEQ ID NO: 19) CGGGGUGCGCACUGCGCGCAGGUCU; (SEQ ID NO: 20) UGCGCACUGCGCGCAGGUCUAGCCAGGAAG; (SEQ ID NO: 21) ACUGCGCGCAGGUCUAGCCAGGAAGCGGGC; or (SEQ ID NO: 64) ACCCGACCCCGUCCCAACCCCGCGU.


19. The method according to claim 1, wherein the antisense agent is capable of binding to a sequence element required for polyadenylation of the DUX4 gene.
 20. The method according to claim 19, wherein the antisense agent is capable of binding to a sequence element required for polyadenylation of the DUX4 gene but not required for polyadenylation of the DUX4c gene.
 21. The method according to claim 19, wherein the sequence element required for polyadenylation of the DUX4 gene is a polyadenylation signal of the DUX4 gene.
 22. The method according to claim 1, wherein the antisense agent is configured to bind to at least about 10 bases, at least about 15 bases, at least about 20 bases, at least about 25 bases, at least about 30 bases, between about 10 and about 40 consecutive bases, or between about 20 and about 30 consecutive bases, of the following DUX4 sequences (SEQ ID NO: 67) or variants thereof having at least about 80%, at least about 90% or at least about 95% sequence identity to said sequence: (SEQ ID NO: 67) acatctcctggatgattagttcagagatatattaaaatgccccctccctgtggatcctatagaaga.


23. The method according to claim 1, wherein the antisense agent comprises a sequence complementary to the following DUX4 sequences (SEQ ID NO: 69) or to variants thereof having at least about 80%, at least about 90%, or at least about 95% sequence identity to said sequence, or to fragments thereof comprising at least 10 bases, or at least 12 bases, at least about 15 bases, at least about 20 bases, or at least about 25 bases of the said sequences or variants: (SEQ ID NO: 69) agttcagagatatattaaaatgccc.


24. The method according to claim 1, where the antisense agent is anti-DUX4 and comprises the sequence (SEQ ID NO: 65) or variants thereof having at least about 80%, at least about 90%, or at least about 95% sequence identity to said sequence, or fragments thereof comprising at least about 10 bases, at least about 12 bases, at least about 15 bases, at least about 20 bases, or at least about 25 bases of said sequence or variants: GGGCAUUUUAAUAUAUCUCUGAACU. (SEQ ID NO: 65)


25. The method according to claim 1, wherein the composition or formulation is a pharmaceutical composition further comprising one or more pharmaceutically acceptable carriers.
 26. The method according to claim 1, wherein the host cell is a myoblast or a myoblast precursor derived from the subject. 